diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp.Abstractions/Configuration/McpToolOptions.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp.Abstractions/Configuration/McpToolOptions.cs
new file mode 100644
index 00000000000..70147bdc2b7
--- /dev/null
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp.Abstractions/Configuration/McpToolOptions.cs
@@ -0,0 +1,25 @@
+namespace HotChocolate.Adapters.Mcp.Configuration;
+
+/// <summary>
+/// Holds the per-schema options that control how MCP tools are generated from operations.
+/// </summary>
+public sealed class McpToolOptions
+{
+    /// <summary>
+    /// Gets or sets a value indicating whether named input object types are emitted in a tool's
+    /// input schema as JSON Schema definitions (<c>$defs</c>) referenced through <c>$ref</c>.
+    /// <para>
+    /// When <c>true</c> (the default), each named input object type is emitted once under
+    /// <c>$defs</c> and referenced by <c>$ref</c>. This is the only way to represent recursive
+    /// input types (such as filter inputs that reference themselves through <c>and</c>/<c>or</c>)
+    /// in a finite schema.
+    /// </para>
+    /// <para>
+    /// When <c>false</c>, input object types are inlined. This suits MCP clients that do not
+    /// support JSON Schema references. Where a type refers to itself, that point is collapsed to
+    /// a generic object (<c>{ "type": "object" }</c>) and the rest of the schema keeps its full
+    /// structure.
+    /// </para>
+    /// </summary>
+    public bool UseJsonSchemaReferences { get; set; } = true;
+}
diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/InputValueDefinitionExtensions.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/InputValueDefinitionExtensions.cs
index cdf48b208ac..2fb34226f4e 100644
--- a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/InputValueDefinitionExtensions.cs
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/InputValueDefinitionExtensions.cs
@@ -5,7 +5,9 @@ namespace HotChocolate.Adapters.Mcp.Extensions;
 
 internal static class InputValueDefinitionExtensions
 {
-    public static JsonSchema ToJsonSchema(this IInputValueDefinition inputField)
+    public static JsonSchema ToJsonSchema(
+        this IInputValueDefinition inputField,
+        JsonSchemaContext? context = null)
     {
         var type = inputField.Type;
         var schemaBuilder =
@@ -13,7 +15,8 @@ public static JsonSchema ToJsonSchema(this IInputValueDefinition inputField)
                 isOneOf: inputField.DeclaringMember is IInputObjectTypeDefinition
                 {
                     IsOneOf: true
-                });
+                },
+                context);
 
         // Description.
         if (inputField.Description is not null)
diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/JsonSchemaContext.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/JsonSchemaContext.cs
new file mode 100644
index 00000000000..54b108195bd
--- /dev/null
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/JsonSchemaContext.cs
@@ -0,0 +1,29 @@
+using Json.Schema;
+
+namespace HotChocolate.Adapters.Mcp.Extensions;
+
+/// <summary>
+/// Carries the state shared across a single JSON schema generation walk: the accumulated
+/// definitions, the set of input object types currently being expanded (for cycle detection),
+/// and whether references are used.
+/// </summary>
+internal sealed class JsonSchemaContext
+{
+    /// <summary>
+    /// Gets the named input object type definitions discovered during the walk, keyed by type
+    /// name. These are emitted at the root of the schema under <c>$defs</c>.
+    /// </summary>
+    public Dictionary<string, JsonSchema> Defs { get; } = new(StringComparer.Ordinal);
+
+    /// <summary>
+    /// Gets the names of the input object types currently being expanded on the active path.
+    /// Used to detect cycles so the walk terminates on self-referencing types.
+    /// </summary>
+    public HashSet<string> Building { get; } = new(StringComparer.Ordinal);
+
+    /// <summary>
+    /// Gets a value indicating whether named input object types are emitted as <c>$defs</c>
+    /// referenced through <c>$ref</c> (<c>true</c>) or inlined (<c>false</c>).
+    /// </summary>
+    public bool UseReferences { get; init; } = true;
+}
diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/ServiceCollectionExtensions.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/ServiceCollectionExtensions.cs
index 417e80d075e..3a4d26917c5 100644
--- a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/ServiceCollectionExtensions.cs
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/ServiceCollectionExtensions.cs
@@ -58,10 +58,25 @@ public static void AddMcpSchemaServices(
         var mcpManager = applicationServices.GetRequiredService<McpManager>();
         var setup = mcpManager.GetSetup(schemaName);
 
-        services
-            .AddLogging()
-            .TryAddSingleton(
-                static sp => new OperationToolFactory(sp.GetRequiredService<ISchemaDefinition>()));
+        services.AddLogging();
+
+        services.TryAddSingleton(
+            static sp =>
+            {
+                var toolOptions = new McpToolOptions();
+
+                foreach (var configure in sp.GetServices<Action<McpToolOptions>>())
+                {
+                    configure(toolOptions);
+                }
+
+                return toolOptions;
+            });
+
+        services.TryAddSingleton(
+            static sp => new OperationToolFactory(
+                sp.GetRequiredService<ISchemaDefinition>(),
+                sp.GetRequiredService<McpToolOptions>()));
 
         services.TryAddSingleton<IMcpDiagnosticEvents>(sp =>
         {
diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/TypeExtensions.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/TypeExtensions.cs
index 481a1e3e219..edda51e62ee 100644
--- a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/TypeExtensions.cs
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/Extensions/TypeExtensions.cs
@@ -8,14 +8,30 @@ namespace HotChocolate.Adapters.Mcp.Extensions;
 
 internal static class TypeExtensions
 {
-    public static JsonSchemaBuilder ToJsonSchemaBuilder(this IType type, bool isOneOf = false)
+    public static JsonSchemaBuilder ToJsonSchemaBuilder(
+        this IType type,
+        bool isOneOf = false,
+        JsonSchemaContext? context = null)
     {
+        var namedType = type.NullableType();
+        var isNullable = !type.IsNonNullType() && !isOneOf;
+
+        // Named input object types are emitted once under $defs and referenced through $ref.
+        // This is the only way to represent a self-referencing input type (such as a filter
+        // input) in a finite schema.
+        if (context is { UseReferences: true }
+            && namedType is IInputObjectTypeDefinition inputObjectReference)
+        {
+            RegisterInputObjectDef(inputObjectReference, context);
+            return RefSchema(inputObjectReference.Name, isNullable);
+        }
+
         var schemaBuilder = new JsonSchemaBuilder();
 
         // Type.
         var jsonType = type.GetJsonSchemaValueType();
 
-        if (!type.IsNonNullType() && !isOneOf)
+        if (isNullable)
         {
             // Nullability.
             jsonType |= SchemaValueType.Null;
@@ -47,7 +63,7 @@ public static JsonSchemaBuilder ToJsonSchemaBuilder(this IType type, bool isOneO
             schemaBuilder.Pattern(pattern);
         }
 
-        switch (type.NullableType())
+        switch (namedType)
         {
             case IEnumTypeDefinition enumType:
                 // Enum values.
@@ -67,58 +83,109 @@ public static JsonSchemaBuilder ToJsonSchemaBuilder(this IType type, bool isOneO
                 break;
 
             case IInputObjectTypeDefinition inputObjectType:
-                // Object properties.
-                var objectProperties = new Dictionary<string, JsonSchema>();
-                var requiredObjectProperties = new List<string>();
-
-                foreach (var field in inputObjectType.Fields)
+                // References are disabled, so the type is inlined. The cycle guard keeps the walk
+                // finite by collapsing a self-reference to the generic object schema already set.
+                // A false result means the type is already being expanded on the current path.
+                if (context?.Building.Add(inputObjectType.Name) == false)
                 {
-                    var fieldSchema = field.ToJsonSchema();
-
-                    objectProperties.Add(field.Name, fieldSchema);
-
-                    if (field.Type.IsNonNullType() && field.DefaultValue is null)
-                    {
-                        requiredObjectProperties.Add(field.Name);
-                    }
+                    break;
                 }
 
-                // OneOf.
-                if (inputObjectType.IsOneOf)
-                {
-                    List<JsonSchema> oneOfSchemas = [];
-
-                    foreach (var (propertyName, propertySchema) in objectProperties)
-                    {
-                        var oneOfSchema = new JsonSchemaBuilder();
-
-                        oneOfSchema
-                            .Type(SchemaValueType.Object)
-                            .Properties((propertyName, propertySchema))
-                            .Required(propertyName);
-
-                        oneOfSchemas.Add(oneOfSchema.Build());
-                    }
-
-                    schemaBuilder.OneOf(oneOfSchemas);
-                }
-                else
-                {
-                    schemaBuilder.Properties(objectProperties);
-                    schemaBuilder.Required(requiredObjectProperties);
-                }
+                PopulateInputObjectMembers(schemaBuilder, inputObjectType, context);
 
+                context?.Building.Remove(inputObjectType.Name);
                 break;
 
             case ListType listType:
                 // Array items.
-                schemaBuilder.Items(listType.ElementType().ToJsonSchemaBuilder());
+                schemaBuilder.Items(listType.ElementType().ToJsonSchemaBuilder(context: context));
                 break;
         }
 
         return schemaBuilder;
     }
 
+    private static void RegisterInputObjectDef(
+        IInputObjectTypeDefinition inputObjectType,
+        JsonSchemaContext context)
+    {
+        var name = inputObjectType.Name;
+
+        // The definition name is reserved before its members are expanded so that a field
+        // referencing the same type resolves to a $ref instead of recursing.
+        if (context.Defs.ContainsKey(name) || !context.Building.Add(name))
+        {
+            return;
+        }
+
+        var defBuilder = new JsonSchemaBuilder().Type(SchemaValueType.Object);
+        PopulateInputObjectMembers(defBuilder, inputObjectType, context);
+
+        context.Defs[name] = defBuilder;
+        context.Building.Remove(name);
+    }
+
+    private static JsonSchemaBuilder RefSchema(string typeName, bool isNullable)
+    {
+        var reference = new JsonSchemaBuilder().Ref("#/$defs/" + typeName);
+
+        if (!isNullable)
+        {
+            return reference;
+        }
+
+        // A bare $ref cannot also permit null, so a nullable reference is expressed as an anyOf.
+        return new JsonSchemaBuilder()
+            .AnyOf(reference, new JsonSchemaBuilder().Type(SchemaValueType.Null));
+    }
+
+    private static void PopulateInputObjectMembers(
+        JsonSchemaBuilder schemaBuilder,
+        IInputObjectTypeDefinition inputObjectType,
+        JsonSchemaContext? context)
+    {
+        // Object properties.
+        var objectProperties = new Dictionary<string, JsonSchema>();
+        var requiredObjectProperties = new List<string>();
+
+        foreach (var field in inputObjectType.Fields)
+        {
+            var fieldSchema = field.ToJsonSchema(context);
+
+            objectProperties.Add(field.Name, fieldSchema);
+
+            if (field.Type.IsNonNullType() && field.DefaultValue is null)
+            {
+                requiredObjectProperties.Add(field.Name);
+            }
+        }
+
+        // OneOf.
+        if (inputObjectType.IsOneOf)
+        {
+            List<JsonSchema> oneOfSchemas = [];
+
+            foreach (var (propertyName, propertySchema) in objectProperties)
+            {
+                var oneOfSchema = new JsonSchemaBuilder();
+
+                oneOfSchema
+                    .Type(SchemaValueType.Object)
+                    .Properties((propertyName, propertySchema))
+                    .Required(propertyName);
+
+                oneOfSchemas.Add(oneOfSchema.Build());
+            }
+
+            schemaBuilder.OneOf(oneOfSchemas);
+        }
+        else
+        {
+            schemaBuilder.Properties(objectProperties);
+            schemaBuilder.Required(requiredObjectProperties);
+        }
+    }
+
     private static SchemaValueType GetJsonSchemaValueType(this IType type)
     {
         return type switch
diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/OperationToolFactory.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/OperationToolFactory.cs
index bd3ff587796..ac5b5e541ae 100644
--- a/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/OperationToolFactory.cs
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp.Core/OperationToolFactory.cs
@@ -1,6 +1,7 @@
 using System.Collections.Frozen;
 using System.Text;
 using System.Text.Json.Nodes;
+using HotChocolate.Adapters.Mcp.Configuration;
 using HotChocolate.Adapters.Mcp.Extensions;
 using HotChocolate.Adapters.Mcp.Storage;
 using HotChocolate.Language;
@@ -13,7 +14,7 @@
 
 namespace HotChocolate.Adapters.Mcp;
 
-internal sealed class OperationToolFactory(ISchemaDefinition schema)
+internal sealed class OperationToolFactory(ISchemaDefinition schema, McpToolOptions options)
 {
     private static readonly Walker s_walker = new();
 
@@ -137,11 +138,12 @@ private JsonSchema CreateInputSchema(OperationDefinitionNode operation)
     {
         var properties = new Dictionary<string, JsonSchema>();
         var requiredProperties = new List<string>();
+        var context = new JsonSchemaContext { UseReferences = options.UseJsonSchemaReferences };
 
         foreach (var variableNode in operation.VariableDefinitions)
         {
             var type = variableNode.Type.ToType(schema);
-            var propertyBuilder = type.ToJsonSchemaBuilder();
+            var propertyBuilder = type.ToJsonSchemaBuilder(context: context);
             var variableName = variableNode.Variable.Name.Value;
 
             // Description.
@@ -165,12 +167,22 @@ private JsonSchema CreateInputSchema(OperationDefinitionNode operation)
             properties.Add(variableName, propertyBuilder);
         }
 
-        return
+        var schemaBuilder =
             new JsonSchemaBuilder()
                 .Type(SchemaValueType.Object)
                 .Properties(properties)
-                .Required(requiredProperties)
-                .Build();
+                .Required(requiredProperties);
+
+        // Definitions, emitted in a stable order so the schema is deterministic.
+        if (context.Defs.Count > 0)
+        {
+            schemaBuilder.Defs(
+                context.Defs
+                    .OrderBy(definition => definition.Key, StringComparer.Ordinal)
+                    .ToDictionary());
+        }
+
+        return schemaBuilder.Build();
     }
 
     private static JsonSchema CreateOutputSchema(JsonSchema dataSchema)
diff --git a/src/HotChocolate/Adapters/src/Adapters.Mcp/Extensions/McpRequestExecutorBuilderExtensions.cs b/src/HotChocolate/Adapters/src/Adapters.Mcp/Extensions/McpRequestExecutorBuilderExtensions.cs
index f2a7f050a9d..ab143704b8d 100644
--- a/src/HotChocolate/Adapters/src/Adapters.Mcp/Extensions/McpRequestExecutorBuilderExtensions.cs
+++ b/src/HotChocolate/Adapters/src/Adapters.Mcp/Extensions/McpRequestExecutorBuilderExtensions.cs
@@ -42,6 +42,36 @@ public static IRequestExecutorBuilder AddMcp(
         return builder;
     }
 
+    /// <summary>
+    /// Modifies the options that control how MCP tools are generated from operations.
+    /// </summary>
+    /// <param name="builder">
+    /// The <see cref="IRequestExecutorBuilder"/>.
+    /// </param>
+    /// <param name="configure">
+    /// A delegate to modify the <see cref="McpToolOptions"/>.
+    /// </param>
+    /// <returns>
+    /// Returns the <see cref="IRequestExecutorBuilder"/> so that configuration can be chained.
+    /// </returns>
+    /// <exception cref="ArgumentNullException">
+    /// The <paramref name="builder"/> is <c>null</c>.
+    /// </exception>
+    /// <exception cref="ArgumentNullException">
+    /// The <paramref name="configure"/> is <c>null</c>.
+    /// </exception>
+    public static IRequestExecutorBuilder ModifyMcpToolOptions(
+        this IRequestExecutorBuilder builder,
+        Action<McpToolOptions> configure)
+    {
+        ArgumentNullException.ThrowIfNull(builder);
+        ArgumentNullException.ThrowIfNull(configure);
+
+        builder.ConfigureSchemaServices(services => services.AddSingleton(configure));
+
+        return builder;
+    }
+
     /// <summary>
     /// Adds an MCP storage to the schema.
     /// </summary>
diff --git a/src/HotChocolate/Adapters/src/Fusion.Adapters.Mcp/Extensions/FusionGatewayBuilderExtensions.cs b/src/HotChocolate/Adapters/src/Fusion.Adapters.Mcp/Extensions/FusionGatewayBuilderExtensions.cs
index 3725e573b30..fda96ecf28d 100644
--- a/src/HotChocolate/Adapters/src/Fusion.Adapters.Mcp/Extensions/FusionGatewayBuilderExtensions.cs
+++ b/src/HotChocolate/Adapters/src/Fusion.Adapters.Mcp/Extensions/FusionGatewayBuilderExtensions.cs
@@ -39,6 +39,36 @@ public static IFusionGatewayBuilder AddMcp(
         return builder;
     }
 
+    /// <summary>
+    /// Modifies the options that control how MCP tools are generated from operations.
+    /// </summary>
+    /// <param name="builder">
+    /// The <see cref="IFusionGatewayBuilder"/>.
+    /// </param>
+    /// <param name="configure">
+    /// A delegate to modify the <see cref="McpToolOptions"/>.
+    /// </param>
+    /// <returns>
+    /// Returns the <see cref="IFusionGatewayBuilder"/> so that configuration can be chained.
+    /// </returns>
+    /// <exception cref="ArgumentNullException">
+    /// The <paramref name="builder"/> is <c>null</c>.
+    /// </exception>
+    /// <exception cref="ArgumentNullException">
+    /// The <paramref name="configure"/> is <c>null</c>.
+    /// </exception>
+    public static IFusionGatewayBuilder ModifyMcpToolOptions(
+        this IFusionGatewayBuilder builder,
+        Action<McpToolOptions> configure)
+    {
+        ArgumentNullException.ThrowIfNull(builder);
+        ArgumentNullException.ThrowIfNull(configure);
+
+        builder.ConfigureSchemaServices((_, services) => services.AddSingleton(configure));
+
+        return builder;
+    }
+
     /// <summary>
     /// Adds an MCP storage to the gateway.
     /// </summary>
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/OperationToolFactoryTests.cs b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/OperationToolFactoryTests.cs
index 20e40942a82..910eb206021 100644
--- a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/OperationToolFactoryTests.cs
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/OperationToolFactoryTests.cs
@@ -1,3 +1,4 @@
+using HotChocolate.Adapters.Mcp.Configuration;
 using HotChocolate.Adapters.Mcp.Storage;
 using HotChocolate.Language;
 using HotChocolate.Types;
@@ -16,7 +17,7 @@ static OperationTool Action()
             var document = Utf8GraphQLParser.Parse("fragment Fragment on Type { field }");
             var toolDefinition = new OperationToolDefinition(document);
 
-            return new OperationToolFactory(schema).CreateTool(toolDefinition);
+            return new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         }
 
         // assert
@@ -48,7 +49,7 @@ query Operation2 {
                 """);
             var toolDefinition = new OperationToolDefinition(document);
 
-            return new OperationToolFactory(schema).CreateTool(toolDefinition);
+            return new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         }
 
         // assert
@@ -74,7 +75,7 @@ query GetBooks {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -104,7 +105,7 @@ mutation AddBook {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -134,7 +135,7 @@ subscription BookAdded {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -167,7 +168,7 @@ query GetBooks {
             };
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal("Custom Title", tool.Tool.Title);
@@ -195,7 +196,7 @@ mutation AddBook {
             };
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -232,7 +233,7 @@ mutation AddBook {
             };
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -252,7 +253,7 @@ public void CreateTool_WithNullableVariables_CreatesCorrectSchema()
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -270,7 +271,7 @@ public void CreateTool_WithNonNullableVariables_CreatesCorrectSchema()
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -288,7 +289,7 @@ public void CreateTool_WithDefaultedVariables_CreatesCorrectSchema()
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -306,7 +307,7 @@ public void CreateTool_WithComplexVariables_CreatesCorrectSchema()
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -314,6 +315,72 @@ public void CreateTool_WithComplexVariables_CreatesCorrectSchema()
         mcpTool.OutputSchema.MatchSnapshot(postFix: "Output", extension: ".json");
     }
 
+    // The same non-recursive fixture, with references off, must inline every nested input
+    // object and emit no $ref/$defs.
+    [Fact]
+    public void CreateTool_WithComplexVariables_ReferencesDisabled_InlinesWithoutReferences()
+    {
+        // arrange
+        var schema = CreateSchema(s => s.AddType(new DurationType(DurationFormat.DotNet)));
+        var document = Utf8GraphQLParser.Parse(
+            File.ReadAllText("__resources__/GetWithComplexVariables.graphql"));
+        var toolDefinition = new OperationToolDefinition(document);
+
+        // act
+        var tool =
+            new OperationToolFactory(schema, new McpToolOptions { UseJsonSchemaReferences = false })
+                .CreateTool(toolDefinition);
+
+        // assert
+        tool.Tool.InputSchema.MatchSnapshot(extension: ".json");
+    }
+
+    // An input object that references itself (as filter inputs do via and/or) is finite
+    // only when emitted through $defs/$ref.
+    [Fact]
+    public void CreateTool_SelfReferencingInputVariable_UsesReferences()
+    {
+        // arrange
+        var schema = CreateRecursiveFilterSchema();
+        var document = Utf8GraphQLParser.Parse(
+            """
+            query GetWithRecursiveFilter($filter: RecursiveFilterInput) {
+                withRecursiveFilter(filter: $filter)
+            }
+            """);
+        var toolDefinition = new OperationToolDefinition(document);
+
+        // act
+        var tool =
+            new OperationToolFactory(schema, new McpToolOptions())
+                .CreateTool(toolDefinition);
+
+        // assert
+        tool.Tool.InputSchema.MatchSnapshot(extension: ".json");
+    }
+
+    [Fact]
+    public void CreateTool_SelfReferencingInputVariable_ReferencesDisabled_Inlines()
+    {
+        // arrange
+        var schema = CreateRecursiveFilterSchema();
+        var document = Utf8GraphQLParser.Parse(
+            """
+            query GetWithRecursiveFilter($filter: RecursiveFilterInput) {
+                withRecursiveFilter(filter: $filter)
+            }
+            """);
+        var toolDefinition = new OperationToolDefinition(document);
+
+        // act
+        var tool =
+            new OperationToolFactory(schema, new McpToolOptions { UseJsonSchemaReferences = false })
+                .CreateTool(toolDefinition);
+
+        // assert
+        tool.Tool.InputSchema.MatchSnapshot(extension: ".json");
+    }
+
     [Fact]
     public void CreateTool_WithInterfaceType_CreatesCorrectOutputSchema()
     {
@@ -337,7 +404,7 @@ ... on Dog {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         tool.Tool.OutputSchema.MatchSnapshot(extension: ".json");
@@ -365,7 +432,7 @@ ... on Dog {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         tool.Tool.OutputSchema.MatchSnapshot(extension: ".json");
@@ -381,7 +448,7 @@ public void CreateTool_WithSkipAndInclude_CreatesCorrectOutputSchema()
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         tool.Tool.OutputSchema.MatchSnapshot(extension: ".json");
@@ -401,7 +468,7 @@ public void CreateTool_McpToolAnnotationsDestructiveHintImplementationFirst_Sets
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(destructiveHint, tool.Tool.Annotations?.DestructiveHint);
@@ -446,7 +513,7 @@ public void CreateTool_McpToolAnnotationsCodeFirst_SetsCorrectHint(
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(destructiveHint, tool.Tool.Annotations?.DestructiveHint);
@@ -482,7 +549,7 @@ type Mutation {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(destructiveHint, tool.Tool.Annotations?.DestructiveHint);
@@ -502,7 +569,7 @@ public void CreateTool_McpToolAnnotationsIdempotentHintImplementationFirst_SetsC
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(idempotentHint, tool.Tool.Annotations?.IdempotentHint);
@@ -547,7 +614,7 @@ public void CreateTool_McpToolAnnotationsIdempotentHintCodeFirst_SetsCorrectHint
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(idempotentHint, tool.Tool.Annotations?.IdempotentHint);
@@ -583,7 +650,7 @@ type Mutation {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(idempotentHint, tool.Tool.Annotations?.IdempotentHint);
@@ -605,7 +672,7 @@ public void CreateTool_McpToolAnnotationsOpenWorldHintImplementationFirst_SetsCo
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(openWorldHint, tool.Tool.Annotations?.OpenWorldHint);
@@ -661,7 +728,7 @@ public void CreateTool_McpToolAnnotationsOpenWorldHintCodeFirst_SetsCorrectHint(
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(openWorldHint, tool.Tool.Annotations?.OpenWorldHint);
@@ -710,7 +777,7 @@ type ExplicitClosedWorld {
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
 
         // assert
         Assert.Equal(openWorldHint, tool.Tool.Annotations?.OpenWorldHint);
@@ -727,7 +794,7 @@ public void CreateTool_McpToolAnnotationsWithFragment_SetsCorrectHints()
         var toolDefinition = new OperationToolDefinition(document);
 
         // act
-        var tool = new OperationToolFactory(schema).CreateTool(toolDefinition);
+        var tool = new OperationToolFactory(schema, new McpToolOptions()).CreateTool(toolDefinition);
         var mcpTool = tool.Tool;
 
         // assert
@@ -756,4 +823,28 @@ private static Schema CreateSchema(Action<ISchemaBuilder>? configure = null)
 
         return schemaBuilder.Create();
     }
+
+    private static Schema CreateRecursiveFilterSchema()
+    {
+        return SchemaBuilder
+            .New()
+            .AddMcp()
+            .AddQueryType<RecursiveFilterQuery>()
+            .ModifyOptions(o => o.StrictValidation = false)
+            .Create();
+    }
+
+    public sealed class RecursiveFilterQuery
+    {
+        public int GetWithRecursiveFilter(RecursiveFilter? filter) => filter is null ? 0 : 1;
+    }
+
+    public sealed class RecursiveFilter
+    {
+        public RecursiveFilter[]? And { get; set; }
+
+        public RecursiveFilter[]? Or { get; set; }
+
+        public string? Name { get; set; }
+    }
 }
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_SelfReferencingInputVariable_ReferencesDisabled_Inlines.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_SelfReferencingInputVariable_ReferencesDisabled_Inlines.json
new file mode 100644
index 00000000000..8bf18c4f7e5
--- /dev/null
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_SelfReferencingInputVariable_ReferencesDisabled_Inlines.json
@@ -0,0 +1,39 @@
+{
+  "type": "object",
+  "properties": {
+    "filter": {
+      "type": [
+        "object",
+        "null"
+      ],
+      "properties": {
+        "and": {
+          "type": [
+            "array",
+            "null"
+          ],
+          "items": {
+            "type": "object"
+          }
+        },
+        "or": {
+          "type": [
+            "array",
+            "null"
+          ],
+          "items": {
+            "type": "object"
+          }
+        },
+        "name": {
+          "type": [
+            "string",
+            "null"
+          ]
+        }
+      },
+      "required": []
+    }
+  },
+  "required": []
+}
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_SelfReferencingInputVariable_UsesReferences.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_SelfReferencingInputVariable_UsesReferences.json
new file mode 100644
index 00000000000..49e0c6c9d52
--- /dev/null
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_SelfReferencingInputVariable_UsesReferences.json
@@ -0,0 +1,48 @@
+{
+  "type": "object",
+  "properties": {
+    "filter": {
+      "anyOf": [
+        {
+          "$ref": "#/$defs/RecursiveFilterInput"
+        },
+        {
+          "type": "null"
+        }
+      ]
+    }
+  },
+  "required": [],
+  "$defs": {
+    "RecursiveFilterInput": {
+      "type": "object",
+      "properties": {
+        "and": {
+          "type": [
+            "array",
+            "null"
+          ],
+          "items": {
+            "$ref": "#/$defs/RecursiveFilterInput"
+          }
+        },
+        "or": {
+          "type": [
+            "array",
+            "null"
+          ],
+          "items": {
+            "$ref": "#/$defs/RecursiveFilterInput"
+          }
+        },
+        "name": {
+          "type": [
+            "string",
+            "null"
+          ]
+        }
+      },
+      "required": []
+    }
+  }
+}
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_CreatesCorrectSchema_Input.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_CreatesCorrectSchema_Input.json
index 6b2f2f3a596..f5898c1c400 100644
--- a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_CreatesCorrectSchema_Input.json
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_CreatesCorrectSchema_Input.json
@@ -4,48 +4,7 @@
     "list": {
       "type": "array",
       "items": {
-        "type": "object",
-        "properties": {
-          "field1A": {
-            "type": "object",
-            "properties": {
-              "field1B": {
-                "type": "array",
-                "items": {
-                  "type": "object",
-                  "properties": {
-                    "field1C": {
-                      "type": [
-                        "string",
-                        "null"
-                      ],
-                      "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
-                      "description": "field1C description",
-                      "default": "12:00:00"
-                    }
-                  },
-                  "required": []
-                },
-                "description": "field1B description",
-                "default": [
-                  {
-                    "field1C": "12:00:00"
-                  }
-                ]
-              }
-            },
-            "required": [],
-            "description": "field1A description",
-            "default": {
-              "field1B": [
-                {
-                  "field1C": "12:00:00"
-                }
-              ]
-            }
-          }
-        },
-        "required": []
+        "$ref": "#/$defs/Object1ComplexInput"
       },
       "description": "Complex list",
       "default": [
@@ -61,48 +20,7 @@
       ]
     },
     "object": {
-      "type": "object",
-      "properties": {
-        "field1A": {
-          "type": "object",
-          "properties": {
-            "field1B": {
-              "type": "array",
-              "items": {
-                "type": "object",
-                "properties": {
-                  "field1C": {
-                    "type": [
-                      "string",
-                      "null"
-                    ],
-                    "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
-                    "description": "field1C description",
-                    "default": "12:00:00"
-                  }
-                },
-                "required": []
-              },
-              "description": "field1B description",
-              "default": [
-                {
-                  "field1C": "12:00:00"
-                }
-              ]
-            }
-          },
-          "required": [],
-          "description": "field1A description",
-          "default": {
-            "field1B": [
-              {
-                "field1C": "12:00:00"
-              }
-            ]
-          }
-        }
-      },
-      "required": [],
+      "$ref": "#/$defs/Object1ComplexInput",
       "description": "Complex object",
       "default": {
         "field1A": {
@@ -139,40 +57,70 @@
       ]
     },
     "objectWithNullDefault": {
-      "type": [
-        "object",
-        "null"
+      "anyOf": [
+        {
+          "$ref": "#/$defs/Object1ComplexInput"
+        },
+        {
+          "type": "null"
+        }
       ],
-      "properties": {
+      "description": "Object with null default",
+      "default": {
         "field1A": {
-          "type": "object",
-          "properties": {
-            "field1B": {
-              "type": "array",
-              "items": {
-                "type": "object",
-                "properties": {
-                  "field1C": {
-                    "type": [
-                      "string",
-                      "null"
-                    ],
-                    "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
-                    "description": "field1C description",
-                    "default": "12:00:00"
-                  }
-                },
-                "required": []
-              },
-              "description": "field1B description",
-              "default": [
-                {
-                  "field1C": "12:00:00"
-                }
-              ]
+          "field1B": [
+            {
+              "field1C": null
             }
-          },
-          "required": [],
+          ]
+        }
+      }
+    },
+    "oneOf": {
+      "$ref": "#/$defs/OneOfInput",
+      "description": "OneOf",
+      "default": {
+        "field1": 1
+      }
+    },
+    "oneOfList": {
+      "type": "array",
+      "items": {
+        "$ref": "#/$defs/OneOfInput"
+      },
+      "description": "OneOf list",
+      "default": [
+        {
+          "field1": 1
+        },
+        {
+          "field2": "default"
+        }
+      ]
+    },
+    "objectWithOneOfField": {
+      "$ref": "#/$defs/ObjectWithOneOfFieldInput",
+      "description": "Object with OneOf field",
+      "default": {
+        "field": {
+          "field1": 1
+        }
+      }
+    },
+    "durationDotNet": {
+      "type": "string",
+      "pattern": "^-?(?:(?:\\d{1,8})\\.)?(?:[0-1]?\\d|2[0-3]):(?:[0-5]?\\d):(?:[0-5]?\\d)(?:\\.(?:\\d{1,7}))?$",
+      "description": "Duration with DotNet format",
+      "default": "00:05:00"
+    }
+  },
+  "required": [],
+  "$defs": {
+    "Object1ComplexInput": {
+      "type": "object",
+      "properties": {
+        "field1A": {
+          "$ref": "#/$defs/Object2ComplexInput",
           "description": "field1A description",
           "default": {
             "field1B": [
@@ -183,19 +131,55 @@
           }
         }
       },
-      "required": [],
-      "description": "Object with null default",
-      "default": {
-        "field1A": {
-          "field1B": [
+      "required": []
+    },
+    "Object2ComplexInput": {
+      "type": "object",
+      "properties": {
+        "field1B": {
+          "type": "array",
+          "items": {
+            "$ref": "#/$defs/Object3ComplexInput"
+          },
+          "description": "field1B description",
+          "default": [
             {
-              "field1C": null
+              "field1C": "12:00:00"
             }
           ]
         }
-      }
+      },
+      "required": []
     },
-    "oneOf": {
+    "Object3ComplexInput": {
+      "type": "object",
+      "properties": {
+        "field1C": {
+          "type": [
+            "string",
+            "null"
+          ],
+          "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+          "description": "field1C description",
+          "default": "12:00:00"
+        }
+      },
+      "required": []
+    },
+    "ObjectWithOneOfFieldInput": {
+      "type": "object",
+      "properties": {
+        "field": {
+          "$ref": "#/$defs/OneOfInput",
+          "description": "field description",
+          "default": {
+            "field1": 1
+          }
+        }
+      },
+      "required": []
+    },
+    "OneOfInput": {
       "type": "object",
       "oneOf": [
         {
@@ -224,108 +208,7 @@
             "field2"
           ]
         }
-      ],
-      "description": "OneOf",
-      "default": {
-        "field1": 1
-      }
-    },
-    "oneOfList": {
-      "type": "array",
-      "items": {
-        "type": "object",
-        "oneOf": [
-          {
-            "type": "object",
-            "properties": {
-              "field1": {
-                "type": "integer",
-                "minimum": -2147483648,
-                "maximum": 2147483647,
-                "description": "field1 description"
-              }
-            },
-            "required": [
-              "field1"
-            ]
-          },
-          {
-            "type": "object",
-            "properties": {
-              "field2": {
-                "type": "string",
-                "description": "field2 description"
-              }
-            },
-            "required": [
-              "field2"
-            ]
-          }
-        ]
-      },
-      "description": "OneOf list",
-      "default": [
-        {
-          "field1": 1
-        },
-        {
-          "field2": "default"
-        }
       ]
-    },
-    "objectWithOneOfField": {
-      "type": "object",
-      "properties": {
-        "field": {
-          "type": "object",
-          "oneOf": [
-            {
-              "type": "object",
-              "properties": {
-                "field1": {
-                  "type": "integer",
-                  "minimum": -2147483648,
-                  "maximum": 2147483647,
-                  "description": "field1 description"
-                }
-              },
-              "required": [
-                "field1"
-              ]
-            },
-            {
-              "type": "object",
-              "properties": {
-                "field2": {
-                  "type": "string",
-                  "description": "field2 description"
-                }
-              },
-              "required": [
-                "field2"
-              ]
-            }
-          ],
-          "description": "field description",
-          "default": {
-            "field1": 1
-          }
-        }
-      },
-      "required": [],
-      "description": "Object with OneOf field",
-      "default": {
-        "field": {
-          "field1": 1
-        }
-      }
-    },
-    "durationDotNet": {
-      "type": "string",
-      "pattern": "^-?(?:(?:\\d{1,8})\\.)?(?:[0-1]?\\d|2[0-3]):(?:[0-5]?\\d):(?:[0-5]?\\d)(?:\\.(?:\\d{1,7}))?$",
-      "description": "Duration with DotNet format",
-      "default": "00:05:00"
     }
-  },
-  "required": []
+  }
 }
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_ReferencesDisabled_InlinesWithoutReferences.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_ReferencesDisabled_InlinesWithoutReferences.json
new file mode 100644
index 00000000000..6b2f2f3a596
--- /dev/null
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithComplexVariables_ReferencesDisabled_InlinesWithoutReferences.json
@@ -0,0 +1,331 @@
+{
+  "type": "object",
+  "properties": {
+    "list": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "properties": {
+          "field1A": {
+            "type": "object",
+            "properties": {
+              "field1B": {
+                "type": "array",
+                "items": {
+                  "type": "object",
+                  "properties": {
+                    "field1C": {
+                      "type": [
+                        "string",
+                        "null"
+                      ],
+                      "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+                      "description": "field1C description",
+                      "default": "12:00:00"
+                    }
+                  },
+                  "required": []
+                },
+                "description": "field1B description",
+                "default": [
+                  {
+                    "field1C": "12:00:00"
+                  }
+                ]
+              }
+            },
+            "required": [],
+            "description": "field1A description",
+            "default": {
+              "field1B": [
+                {
+                  "field1C": "12:00:00"
+                }
+              ]
+            }
+          }
+        },
+        "required": []
+      },
+      "description": "Complex list",
+      "default": [
+        {
+          "field1A": {
+            "field1B": [
+              {
+                "field1C": "12:00:00"
+              }
+            ]
+          }
+        }
+      ]
+    },
+    "object": {
+      "type": "object",
+      "properties": {
+        "field1A": {
+          "type": "object",
+          "properties": {
+            "field1B": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "field1C": {
+                    "type": [
+                      "string",
+                      "null"
+                    ],
+                    "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+                    "description": "field1C description",
+                    "default": "12:00:00"
+                  }
+                },
+                "required": []
+              },
+              "description": "field1B description",
+              "default": [
+                {
+                  "field1C": "12:00:00"
+                }
+              ]
+            }
+          },
+          "required": [],
+          "description": "field1A description",
+          "default": {
+            "field1B": [
+              {
+                "field1C": "12:00:00"
+              }
+            ]
+          }
+        }
+      },
+      "required": [],
+      "description": "Complex object",
+      "default": {
+        "field1A": {
+          "field1B": [
+            {
+              "field1C": "12:00:00"
+            }
+          ]
+        }
+      }
+    },
+    "nullDefault": {
+      "type": [
+        "string",
+        "null"
+      ],
+      "description": "Null default",
+      "default": null
+    },
+    "listWithNullDefault": {
+      "type": [
+        "array",
+        "null"
+      ],
+      "items": {
+        "type": [
+          "string",
+          "null"
+        ]
+      },
+      "description": "List with null default",
+      "default": [
+        null
+      ]
+    },
+    "objectWithNullDefault": {
+      "type": [
+        "object",
+        "null"
+      ],
+      "properties": {
+        "field1A": {
+          "type": "object",
+          "properties": {
+            "field1B": {
+              "type": "array",
+              "items": {
+                "type": "object",
+                "properties": {
+                  "field1C": {
+                    "type": [
+                      "string",
+                      "null"
+                    ],
+                    "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+                    "description": "field1C description",
+                    "default": "12:00:00"
+                  }
+                },
+                "required": []
+              },
+              "description": "field1B description",
+              "default": [
+                {
+                  "field1C": "12:00:00"
+                }
+              ]
+            }
+          },
+          "required": [],
+          "description": "field1A description",
+          "default": {
+            "field1B": [
+              {
+                "field1C": "12:00:00"
+              }
+            ]
+          }
+        }
+      },
+      "required": [],
+      "description": "Object with null default",
+      "default": {
+        "field1A": {
+          "field1B": [
+            {
+              "field1C": null
+            }
+          ]
+        }
+      }
+    },
+    "oneOf": {
+      "type": "object",
+      "oneOf": [
+        {
+          "type": "object",
+          "properties": {
+            "field1": {
+              "type": "integer",
+              "minimum": -2147483648,
+              "maximum": 2147483647,
+              "description": "field1 description"
+            }
+          },
+          "required": [
+            "field1"
+          ]
+        },
+        {
+          "type": "object",
+          "properties": {
+            "field2": {
+              "type": "string",
+              "description": "field2 description"
+            }
+          },
+          "required": [
+            "field2"
+          ]
+        }
+      ],
+      "description": "OneOf",
+      "default": {
+        "field1": 1
+      }
+    },
+    "oneOfList": {
+      "type": "array",
+      "items": {
+        "type": "object",
+        "oneOf": [
+          {
+            "type": "object",
+            "properties": {
+              "field1": {
+                "type": "integer",
+                "minimum": -2147483648,
+                "maximum": 2147483647,
+                "description": "field1 description"
+              }
+            },
+            "required": [
+              "field1"
+            ]
+          },
+          {
+            "type": "object",
+            "properties": {
+              "field2": {
+                "type": "string",
+                "description": "field2 description"
+              }
+            },
+            "required": [
+              "field2"
+            ]
+          }
+        ]
+      },
+      "description": "OneOf list",
+      "default": [
+        {
+          "field1": 1
+        },
+        {
+          "field2": "default"
+        }
+      ]
+    },
+    "objectWithOneOfField": {
+      "type": "object",
+      "properties": {
+        "field": {
+          "type": "object",
+          "oneOf": [
+            {
+              "type": "object",
+              "properties": {
+                "field1": {
+                  "type": "integer",
+                  "minimum": -2147483648,
+                  "maximum": 2147483647,
+                  "description": "field1 description"
+                }
+              },
+              "required": [
+                "field1"
+              ]
+            },
+            {
+              "type": "object",
+              "properties": {
+                "field2": {
+                  "type": "string",
+                  "description": "field2 description"
+                }
+              },
+              "required": [
+                "field2"
+              ]
+            }
+          ],
+          "description": "field description",
+          "default": {
+            "field1": 1
+          }
+        }
+      },
+      "required": [],
+      "description": "Object with OneOf field",
+      "default": {
+        "field": {
+          "field1": 1
+        }
+      }
+    },
+    "durationDotNet": {
+      "type": "string",
+      "pattern": "^-?(?:(?:\\d{1,8})\\.)?(?:[0-1]?\\d|2[0-3]):(?:[0-5]?\\d):(?:[0-5]?\\d)(?:\\.(?:\\d{1,7}))?$",
+      "description": "Duration with DotNet format",
+      "default": "00:05:00"
+    }
+  },
+  "required": []
+}
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithDefaultedVariables_CreatesCorrectSchema_Input.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithDefaultedVariables_CreatesCorrectSchema_Input.json
index 258fe6022e9..80bf85098be 100644
--- a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithDefaultedVariables_CreatesCorrectSchema_Input.json
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithDefaultedVariables_CreatesCorrectSchema_Input.json
@@ -127,38 +127,7 @@
       "default": 9223372036854775807
     },
     "object": {
-      "type": "object",
-      "properties": {
-        "field1A": {
-          "type": "object",
-          "properties": {
-            "field1B": {
-              "type": "object",
-              "properties": {
-                "field1C": {
-                  "type": "string",
-                  "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
-                  "description": "field1C description",
-                  "default": "12:00:00"
-                }
-              },
-              "required": [],
-              "description": "field1B description",
-              "default": {
-                "field1C": "12:00:00"
-              }
-            }
-          },
-          "required": [],
-          "description": "field1A description",
-          "default": {
-            "field1B": {
-              "field1C": "12:00:00"
-            }
-          }
-        }
-      },
-      "required": [],
+      "$ref": "#/$defs/Object1DefaultedInput",
       "description": "Object description",
       "default": {
         "field1A": {
@@ -233,5 +202,47 @@
       "default": "00000000-0000-0000-0000-000000000000"
     }
   },
-  "required": []
+  "required": [],
+  "$defs": {
+    "Object1DefaultedInput": {
+      "type": "object",
+      "properties": {
+        "field1A": {
+          "$ref": "#/$defs/Object2DefaultedInput",
+          "description": "field1A description",
+          "default": {
+            "field1B": {
+              "field1C": "12:00:00"
+            }
+          }
+        }
+      },
+      "required": []
+    },
+    "Object2DefaultedInput": {
+      "type": "object",
+      "properties": {
+        "field1B": {
+          "$ref": "#/$defs/Object3DefaultedInput",
+          "description": "field1B description",
+          "default": {
+            "field1C": "12:00:00"
+          }
+        }
+      },
+      "required": []
+    },
+    "Object3DefaultedInput": {
+      "type": "object",
+      "properties": {
+        "field1C": {
+          "type": "string",
+          "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+          "description": "field1C description",
+          "default": "12:00:00"
+        }
+      },
+      "required": []
+    }
+  }
 }
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNonNullableVariables_CreatesCorrectSchema_Input.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNonNullableVariables_CreatesCorrectSchema_Input.json
index fbbda38f80a..851e981761f 100644
--- a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNonNullableVariables_CreatesCorrectSchema_Input.json
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNonNullableVariables_CreatesCorrectSchema_Input.json
@@ -106,35 +106,7 @@
       "description": "Long description"
     },
     "object": {
-      "type": "object",
-      "properties": {
-        "field1A": {
-          "type": "object",
-          "properties": {
-            "field1B": {
-              "type": "object",
-              "properties": {
-                "field1C": {
-                  "type": "string",
-                  "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
-                  "description": "field1C description"
-                }
-              },
-              "required": [
-                "field1C"
-              ],
-              "description": "field1B description"
-            }
-          },
-          "required": [
-            "field1B"
-          ],
-          "description": "field1A description"
-        }
-      },
-      "required": [
-        "field1A"
-      ],
+      "$ref": "#/$defs/Object1NonNullableInput",
       "description": "Object description"
     },
     "short": {
@@ -221,5 +193,44 @@
     "uri",
     "url",
     "uuid"
-  ]
+  ],
+  "$defs": {
+    "Object1NonNullableInput": {
+      "type": "object",
+      "properties": {
+        "field1A": {
+          "$ref": "#/$defs/Object2NonNullableInput",
+          "description": "field1A description"
+        }
+      },
+      "required": [
+        "field1A"
+      ]
+    },
+    "Object2NonNullableInput": {
+      "type": "object",
+      "properties": {
+        "field1B": {
+          "$ref": "#/$defs/Object3NonNullableInput",
+          "description": "field1B description"
+        }
+      },
+      "required": [
+        "field1B"
+      ]
+    },
+    "Object3NonNullableInput": {
+      "type": "object",
+      "properties": {
+        "field1C": {
+          "type": "string",
+          "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+          "description": "field1C description"
+        }
+      },
+      "required": [
+        "field1C"
+      ]
+    }
+  }
 }
diff --git a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNullableVariables_CreatesCorrectSchema_Input.json b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNullableVariables_CreatesCorrectSchema_Input.json
index f3e257bbd5d..d34d90cfda3 100644
--- a/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNullableVariables_CreatesCorrectSchema_Input.json
+++ b/src/HotChocolate/Adapters/test/Adapters.Mcp.Tests/__snapshots__/OperationToolFactoryTests.CreateTool_WithNullableVariables_CreatesCorrectSchema_Input.json
@@ -157,41 +157,14 @@
       "description": "Long description"
     },
     "object": {
-      "type": [
-        "object",
-        "null"
-      ],
-      "properties": {
-        "field1A": {
-          "type": [
-            "object",
-            "null"
-          ],
-          "properties": {
-            "field1B": {
-              "type": [
-                "object",
-                "null"
-              ],
-              "properties": {
-                "field1C": {
-                  "type": [
-                    "string",
-                    "null"
-                  ],
-                  "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
-                  "description": "field1C description"
-                }
-              },
-              "required": [],
-              "description": "field1B description"
-            }
-          },
-          "required": [],
-          "description": "field1A description"
+      "anyOf": [
+        {
+          "$ref": "#/$defs/Object1NullableInput"
+        },
+        {
+          "type": "null"
         }
-      },
-      "required": [],
+      ],
       "description": "Object description"
     },
     "short": {
@@ -279,5 +252,55 @@
       "description": "UUID description"
     }
   },
-  "required": []
+  "required": [],
+  "$defs": {
+    "Object1NullableInput": {
+      "type": "object",
+      "properties": {
+        "field1A": {
+          "anyOf": [
+            {
+              "$ref": "#/$defs/Object2NullableInput"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "description": "field1A description"
+        }
+      },
+      "required": []
+    },
+    "Object2NullableInput": {
+      "type": "object",
+      "properties": {
+        "field1B": {
+          "anyOf": [
+            {
+              "$ref": "#/$defs/Object3NullableInput"
+            },
+            {
+              "type": "null"
+            }
+          ],
+          "description": "field1B description"
+        }
+      },
+      "required": []
+    },
+    "Object3NullableInput": {
+      "type": "object",
+      "properties": {
+        "field1C": {
+          "type": [
+            "string",
+            "null"
+          ],
+          "pattern": "^\\d{2}:\\d{2}:\\d{2}(?:\\.\\d{1,9})?$",
+          "description": "field1C description"
+        }
+      },
+      "required": []
+    }
+  }
 }
diff --git a/website/src/docs/fusion/v16/adapters/mcp.md b/website/src/docs/fusion/v16/adapters/mcp.md
index b2306efc0df..1cdb78ab532 100644
--- a/website/src/docs/fusion/v16/adapters/mcp.md
+++ b/website/src/docs/fusion/v16/adapters/mcp.md
@@ -81,6 +81,24 @@ builder
 
 Tools registered through `configureServer` appear alongside the GraphQL-derived tools, so you can mix native MCP tools with operation tools in the same gateway.
 
+## Input Schema References
+
+An operation's variables become a tool's input schema (JSON Schema). When a variable's type is an input object, the adapter emits that type once under `$defs` and references it with `$ref`. References are how a self-referencing input type is represented in a finite schema, for example a filter input whose `and` and `or` fields are lists of the same type.
+
+References are the default and are understood by current MCP clients and agents. Some clients have limited support for JSON Schema references (recursive `$ref` in particular). For those, turn references off with `ModifyMcpToolOptions()`:
+
+```csharp
+builder
+    .AddGraphQLGateway()
+    .AddMcp()
+    .ModifyMcpToolOptions(options =>
+    {
+        options.UseJsonSchemaReferences = false;
+    });
+```
+
+With references disabled, input object types are inlined. Where a type refers to itself, that point is collapsed to a generic object (`{ "type": "object" }`) and the rest of the schema keeps its full structure. Leave references enabled unless a target client cannot resolve `$ref`.
+
 ## Mapping the MCP Endpoint
 
 `MapGraphQLMcp()` accepts two optional arguments:
@@ -185,6 +203,10 @@ Storage is registered but returned no definitions. With Nitro, ensure a publishe
 
 `NitroServiceOptions` is missing one or more of `ApiId`, `ApiKey`, or `Stage`. Set them through the `AddNitro()` configuration delegate or via the `NITRO_API_ID`, `NITRO_API_KEY`, and `NITRO_STAGE` environment variables.
 
+### MCP client rejects or cannot render a tool's input schema
+
+The client may not support JSON Schema references (`$ref`/`$defs`), which the adapter uses for input object types by default. Disable them with `.ModifyMcpToolOptions(options => options.UseJsonSchemaReferences = false)` to inline the schema instead. See [Input Schema References](#input-schema-references).
+
 ## Next Steps
 
 - Author tools and prompts and publish them to a stage in the [Nitro MCP](/docs/nitro/adapters/mcp) section.
diff --git a/website/src/docs/hotchocolate/v16/build/adapters/mcp.md b/website/src/docs/hotchocolate/v16/build/adapters/mcp.md
index 33bc72a5d36..c80b54092e4 100644
--- a/website/src/docs/hotchocolate/v16/build/adapters/mcp.md
+++ b/website/src/docs/hotchocolate/v16/build/adapters/mcp.md
@@ -81,6 +81,24 @@ builder
 
 Tools registered through `configureServer` appear alongside the GraphQL-derived tools, so you can mix native MCP tools with operation tools in the same server.
 
+## Input Schema References
+
+An operation's variables become a tool's input schema (JSON Schema). When a variable's type is an input object, the adapter emits that type once under `$defs` and references it with `$ref`. References are how a self-referencing input type is represented in a finite schema, for example a filter input whose `and` and `or` fields are lists of the same type.
+
+References are the default and are understood by current MCP clients and agents. Some clients have limited support for JSON Schema references (recursive `$ref` in particular). For those, turn references off with `ModifyMcpToolOptions()`:
+
+```csharp
+builder
+    .AddGraphQL()
+    .AddMcp()
+    .ModifyMcpToolOptions(options =>
+    {
+        options.UseJsonSchemaReferences = false;
+    });
+```
+
+With references disabled, input object types are inlined. Where a type refers to itself, that point is collapsed to a generic object (`{ "type": "object" }`) and the rest of the schema keeps its full structure. Leave references enabled unless a target client cannot resolve `$ref`.
+
 ## Mapping the MCP Endpoint
 
 `MapGraphQLMcp()` accepts two optional arguments:
@@ -185,6 +203,10 @@ Storage is registered but returned no definitions. With Nitro, ensure a publishe
 
 `NitroServiceOptions` is missing one or more of `ApiId`, `ApiKey`, or `Stage`. Set them through the `AddNitro()` configuration delegate or via the `NITRO_API_ID`, `NITRO_API_KEY`, and `NITRO_STAGE` environment variables.
 
+### MCP client rejects or cannot render a tool's input schema
+
+The client may not support JSON Schema references (`$ref`/`$defs`), which the adapter uses for input object types by default. Disable them with `.ModifyMcpToolOptions(options => options.UseJsonSchemaReferences = false)` to inline the schema instead. See [Input Schema References](#input-schema-references).
+
 ## Next Steps
 
 - Author tools and prompts and publish them with Nitro in the [Nitro MCP](/docs/nitro/adapters/mcp) section.