diff --git a/packages/start-plugin-core/src/constants.ts b/packages/start-plugin-core/src/constants.ts
index 088c1ad044b..4252d2f0662 100644
--- a/packages/start-plugin-core/src/constants.ts
+++ b/packages/start-plugin-core/src/constants.ts
@@ -18,3 +18,5 @@ export const ENTRY_POINTS = {
   start: '#tanstack-start-entry',
   router: '#tanstack-router-entry',
 } as const
+
+export const TRANSFORM_ID_REGEX = [/\.[cm]?tsx?$/, /\.[cm]?jsx?$/]
diff --git a/packages/start-plugin-core/src/create-server-fn-plugin/plugin.ts b/packages/start-plugin-core/src/create-server-fn-plugin/plugin.ts
index 68884d695bf..25771328ddc 100644
--- a/packages/start-plugin-core/src/create-server-fn-plugin/plugin.ts
+++ b/packages/start-plugin-core/src/create-server-fn-plugin/plugin.ts
@@ -1,4 +1,4 @@
-import { VITE_ENVIRONMENT_NAMES } from '../constants'
+import { TRANSFORM_ID_REGEX, VITE_ENVIRONMENT_NAMES } from '../constants'
 import { ServerFnCompiler } from './compiler'
 import type { LookupConfig, LookupKind } from './compiler'
 import type { CompileStartFrameworkOptions } from '../start-compiler-plugin/compilers'
@@ -81,6 +81,7 @@ export function createServerFnPlugin(
         filter: {
           id: {
             exclude: new RegExp(`${SERVER_FN_LOOKUP}$`),
+            include: TRANSFORM_ID_REGEX,
           },
           code: {
             // TODO apply this plugin with a different filter per environment so that .createMiddleware() calls are not scanned in server env
diff --git a/packages/start-plugin-core/src/start-compiler-plugin/plugin.ts b/packages/start-plugin-core/src/start-compiler-plugin/plugin.ts
index f2dd1893e74..c1f2893c94c 100644
--- a/packages/start-plugin-core/src/start-compiler-plugin/plugin.ts
+++ b/packages/start-plugin-core/src/start-compiler-plugin/plugin.ts
@@ -6,7 +6,7 @@ import { VIRTUAL_MODULES } from '@tanstack/start-server-core'
 import { normalizePath } from 'vite'
 import path from 'pathe'
 import { makeIdFiltersToMatchWithQuery } from '@rolldown/pluginutils'
-import { VITE_ENVIRONMENT_NAMES } from '../constants'
+import { TRANSFORM_ID_REGEX, VITE_ENVIRONMENT_NAMES } from '../constants'
 import { compileStartOutputFactory } from './compilers'
 import { transformFuncs } from './constants'
 import type { ViteEnvironmentNames } from '../constants'
@@ -54,6 +54,7 @@ export function startCompilerPlugin(
       filter: {
         code: tokenRegex,
         id: {
+          include: TRANSFORM_ID_REGEX,
           exclude: [
             VIRTUAL_MODULES.serverFnManifest,
             // N.B. the following files either just re-export or provide the runtime implementation of those functions