diff --git a/.changeset/silly-chairs-rest.md b/.changeset/silly-chairs-rest.md
new file mode 100644
index 0000000000..b56276eaf8
--- /dev/null
+++ b/.changeset/silly-chairs-rest.md
@@ -0,0 +1,5 @@
+---
+'@workflow/nitro': patch
+---
+
+Skip Workflow transforms for generated Nitro build artifacts.
diff --git a/packages/nitro/src/index.test.ts b/packages/nitro/src/index.test.ts
index ca9ecc8d35..4a722986ef 100644
--- a/packages/nitro/src/index.test.ts
+++ b/packages/nitro/src/index.test.ts
@@ -152,6 +152,56 @@ describe('@workflow/nitro builder lifecycle', () => {
   });
 });
 
+describe('@workflow/nitro transform boundaries', () => {
+  it('does not re-transform generated Nitro build artifacts', async () => {
+    const rollupBeforeHooks: Array<(nitro: any, config: any) => void> = [];
+    const nitro = createNitroStub({ routing: true });
+    nitro.hooks.hook = (
+      name: string,
+      hook: (nitro: any, config: any) => void
+    ) => {
+      if (name === 'rollup:before') rollupBeforeHooks.push(hook);
+    };
+
+    const plugins = viteWorkflow();
+    const viteTransform = plugins.find(
+      (plugin) => plugin.name === 'workflow:transform'
+    ) as any;
+    const viteNitro = plugins.find(
+      (plugin) => plugin.name === 'workflow:nitro'
+    ) as any;
+
+    await viteNitro.nitro.setup(nitro);
+
+    const config: { plugins: any[] } = { plugins: [] };
+    for (const hook of rollupBeforeHooks) {
+      hook(nitro, config);
+    }
+    const nitroTransform = config.plugins.find(
+      (plugin: { name?: string }) => plugin.name === 'workflow:transform'
+    );
+
+    const code = `
+      import { WORKFLOW_SERIALIZE, WORKFLOW_DESERIALIZE } from '@workflow/serde';
+      export class Serializable {
+        static [WORKFLOW_SERIALIZE](value) { return value; }
+        static [WORKFLOW_DESERIALIZE]() { return new Serializable(); }
+      }
+    `;
+    const generatedId = '/tmp/.nitro/vite/services/ssr/assets/index.js';
+    const siblingId = '/tmp/.nitro-source/index.js';
+
+    for (const transform of [viteTransform, nitroTransform]) {
+      await expect(
+        transform.transform.call({}, code, generatedId)
+      ).resolves.toBeNull();
+      await expect(
+        transform.transform.call({}, code, siblingId)
+      ).resolves.not.toBeNull();
+    }
+  });
+});
+
 describe('@workflow/nitro world target bundling', () => {
   it('forces workflow SDK packages inline in production builds so aliases can resolve', async () => {
     const rollupBeforeHooks: Array<(nitro: any, config: any) => void> = [];
diff --git a/packages/nitro/src/index.ts b/packages/nitro/src/index.ts
index 15f3e161bc..f6a00b5d53 100644
--- a/packages/nitro/src/index.ts
+++ b/packages/nitro/src/index.ts
@@ -180,9 +180,7 @@ export default {
     const isVercelDeploy =
       !nitro.options.dev && nitro.options.preset === 'vercel';
     const workflowTargetWorld = ensureWorkflowTargetWorldEnv();
-
-    // Pre-built workflow bundles directory - must be excluded from re-transformation
-    const workflowBuildDir = join(nitro.options.buildDir, 'workflow');
+    const nitroBuildDir = `${nitro.options.buildDir.replace(/[\\/]+$/, '')}/`;
 
     nitro.options.alias[WORKFLOW_WORLD_TARGET_MODULE] =
       resolveWorkflowTargetWorldAlias(nitro, workflowTargetWorld);
@@ -193,10 +191,9 @@ export default {
     nitro.hooks.hook('rollup:before', (_nitro: Nitro, config: RollupConfig) => {
       (config.plugins as Array<unknown>).unshift(
         workflowTransformPlugin({
-          // Exclude pre-built workflow bundles from re-transformation
-          // These are already processed and re-processing causes issues like
-          // undefined class references when Nitro's bundler renames variables
-          exclude: [workflowBuildDir],
+          // Nitro build artifacts have already been transformed.
+          // Re-processing them can duplicate class registration.
+          exclude: [nitroBuildDir],
         })
       );
 
diff --git a/packages/nitro/src/vite.ts b/packages/nitro/src/vite.ts
index 6a6116ba18..2c9ba7d334 100644
--- a/packages/nitro/src/vite.ts
+++ b/packages/nitro/src/vite.ts
@@ -9,7 +9,6 @@ import { workflowTransformPlugin } from '@workflow/rollup';
 import { workflowHotUpdatePlugin } from '@workflow/vite';
 import type { Nitro } from 'nitro/types';
 import type {} from 'nitro/vite';
-import { join } from 'pathe';
 import type { Plugin, TransformResult } from 'vite';
 import { LocalBuilder } from './builders.js';
 import type { ModuleOptions } from './index.js';
@@ -18,10 +17,10 @@ import nitroModule from './index.js';
 export function workflow(options?: ModuleOptions): Plugin[] {
   let builder: LocalBuilder;
   let devNitro: Nitro | undefined;
-  let workflowBuildDir: string;
+  let nitroBuildDir: string;
   const enqueue = createBuildQueue();
 
-  // Create a lazy transform plugin that excludes the workflow build directory
+  // Create a lazy transform plugin that excludes Nitro build artifacts.
   // The exclusion path is set during nitro setup, so we need to defer plugin creation
   const lazyTransformPlugin: Plugin = {
     name: 'workflow:transform',
@@ -57,9 +56,9 @@ export function workflow(options?: ModuleOptions): Plugin[] {
     },
     transform(code, id, options) {
       // Delegate to the actual transform plugin with exclusion
-      // workflowBuildDir is set during nitro setup before transforms run
+      // nitroBuildDir is set during nitro setup before transforms run
       const plugin = workflowTransformPlugin({
-        exclude: workflowBuildDir ? [workflowBuildDir] : [],
+        exclude: nitroBuildDir ? [nitroBuildDir] : [],
       });
       const transform = plugin.transform as
         | ((
@@ -79,8 +78,8 @@ export function workflow(options?: ModuleOptions): Plugin[] {
       name: 'workflow:nitro',
       nitro: {
         setup: (nitro: Nitro) => {
-          // Capture the workflow build directory for exclusion
-          workflowBuildDir = join(nitro.options.buildDir, 'workflow');
+          // Capture the Nitro build directory for exclusion
+          nitroBuildDir = `${nitro.options.buildDir.replace(/[\\/]+$/, '')}/`;
           nitro.options.workflow = {
             ...nitro.options.workflow,
             ...options,