diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/build.env b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/build.env
new file mode 100644
index 0000000000..1d658b3c7a
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/build.env
@@ -0,0 +1,5 @@
+CUSTOM_PACK_PROBE=custom
+OTHER_PACK_PROBE=other
+VITE_PACK_PROBE=default
+TSDOWN_PACK_PROBE=compat
+CLI_PACK_PROBE=cli
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/entry.js b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/entry.js
new file mode 100644
index 0000000000..718d38989b
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/entry.js
@@ -0,0 +1 @@
+export const values = [process.env.CUSTOM_PACK_PROBE, process.env.OTHER_PACK_PROBE, process.env.VITE_PACK_PROBE, process.env.TSDOWN_PACK_PROBE, process.env.CLI_PACK_PROBE];
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/package.json b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/package.json
new file mode 100644
index 0000000000..e9489e2986
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/package.json
@@ -0,0 +1 @@
+{"name":"pack-env-prefix","private":true,"type":"module"}
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots.toml b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots.toml
new file mode 100644
index 0000000000..f350be7afa
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots.toml
@@ -0,0 +1,23 @@
+[[case]]
+name = "pack_env_prefix_config"
+vp = ["local", "global"]
+steps = [
+  { argv = ["vp", "pack"], snapshot = false },
+  ["node", "verify.mjs"],
+]
+
+[[case]]
+name = "pack_env_prefix_override"
+vp = ["local", "global"]
+steps = [
+  { argv = ["vp", "pack", "--env-prefix", "CLI_"], snapshot = false },
+  ["node", "verify.mjs", "override"],
+]
+
+[[case]]
+name = "pack_env_prefix_no_config"
+vp = ["local", "global"]
+steps = [
+  { argv = ["vp", "pack", "--no-config", "entry.js", "--env-file", "build.env"], snapshot = false },
+  ["node", "verify.mjs", "no-config"],
+]
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_config.global.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_config.global.md
new file mode 100644
index 0000000000..dde5248ef5
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_config.global.md
@@ -0,0 +1,10 @@
+# pack_env_prefix_config
+
+## `vp pack`
+
+
+## `node verify.mjs`
+
+```
+Environment prefix values and exclusions match.
+```
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_config.local.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_config.local.md
new file mode 100644
index 0000000000..dde5248ef5
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_config.local.md
@@ -0,0 +1,10 @@
+# pack_env_prefix_config
+
+## `vp pack`
+
+
+## `node verify.mjs`
+
+```
+Environment prefix values and exclusions match.
+```
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_no_config.global.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_no_config.global.md
new file mode 100644
index 0000000000..e208c11a4f
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_no_config.global.md
@@ -0,0 +1,10 @@
+# pack_env_prefix_no_config
+
+## `vp pack --no-config entry.js --env-file build.env`
+
+
+## `node verify.mjs no-config`
+
+```
+Environment prefix values and exclusions match.
+```
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_no_config.local.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_no_config.local.md
new file mode 100644
index 0000000000..e208c11a4f
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_no_config.local.md
@@ -0,0 +1,10 @@
+# pack_env_prefix_no_config
+
+## `vp pack --no-config entry.js --env-file build.env`
+
+
+## `node verify.mjs no-config`
+
+```
+Environment prefix values and exclusions match.
+```
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_override.global.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_override.global.md
new file mode 100644
index 0000000000..b0d4136bf4
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_override.global.md
@@ -0,0 +1,10 @@
+# pack_env_prefix_override
+
+## `vp pack --env-prefix CLI_`
+
+
+## `node verify.mjs override`
+
+```
+Environment prefix values and exclusions match.
+```
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_override.local.md b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_override.local.md
new file mode 100644
index 0000000000..b0d4136bf4
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/snapshots/pack_env_prefix_override.local.md
@@ -0,0 +1,10 @@
+# pack_env_prefix_override
+
+## `vp pack --env-prefix CLI_`
+
+
+## `node verify.mjs override`
+
+```
+Environment prefix values and exclusions match.
+```
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/verify.mjs b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/verify.mjs
new file mode 100644
index 0000000000..87aef44603
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/verify.mjs
@@ -0,0 +1,22 @@
+import assert from 'node:assert/strict';
+
+for (const key of ['CUSTOM_PACK_PROBE', 'OTHER_PACK_PROBE', 'VITE_PACK_PROBE', 'TSDOWN_PACK_PROBE', 'CLI_PACK_PROBE']) {
+  delete process.env[key];
+}
+const defaults = [undefined, undefined, 'default', 'compat', undefined];
+const expected = {
+  string: ['custom', undefined, undefined, undefined, undefined],
+  array: ['custom', 'other', undefined, undefined, undefined],
+  empty: [undefined, undefined, undefined, undefined, undefined],
+  defaults,
+};
+if (process.argv[2] === 'no-config') {
+  assert.deepEqual((await import('./dist/entry.mjs')).values, defaults);
+} else {
+  for (const [name, values] of Object.entries(expected)) {
+    assert.deepEqual((await import(`./dist/${name}/entry.mjs`)).values,
+      process.argv[2] === 'override' ? [undefined, undefined, undefined, undefined, 'cli'] : values,
+      name);
+  }
+}
+console.log('Environment prefix values and exclusions match.');
diff --git a/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/vite.config.ts b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/vite.config.ts
new file mode 100644
index 0000000000..689c0084f9
--- /dev/null
+++ b/crates/vp_cli_snapshots/tests/cli_snapshots/fixtures/command_pack_env_prefix/vite.config.ts
@@ -0,0 +1,13 @@
+export default {
+  pack: [
+    { name: 'string', envPrefix: 'CUSTOM_' },
+    { name: 'array', envPrefix: ['CUSTOM_', 'OTHER_'] },
+    { name: 'empty', envPrefix: [] },
+    { name: 'defaults' },
+  ].map(({ name, ...config }) => ({
+    ...config,
+    entry: ['entry.js'],
+    envFile: 'build.env',
+    outDir: `dist/${name}`,
+  })),
+};
diff --git a/packages/cli/src/pack-bin.ts b/packages/cli/src/pack-bin.ts
index 418a96e6a3..23e3acaa82 100644
--- a/packages/cli/src/pack-bin.ts
+++ b/packages/cli/src/pack-bin.ts
@@ -141,9 +141,6 @@ cli
     if (input.length > 0) {
       flags.entry = input;
     }
-    if (flags.envPrefix === undefined) {
-      flags.envPrefix = DEFAULT_ENV_PREFIXES;
-    }
 
     async function runBuild(): Promise<TsdownHandle> {
       const viteConfig =
@@ -163,6 +160,7 @@ cli
         : [viteConfig?.pack ?? {}];
       for (const packConfig of packConfigs) {
         const merged = { ...packConfig, ...flags };
+        merged.envPrefix ??= DEFAULT_ENV_PREFIXES;
         // Keep postcss/lightningcss external to the dts bundle (see plugin doc)
         if (merged.dts) {
           const existingPlugins = Array.isArray(merged.plugins) ? merged.plugins : [];