diff --git a/.changeset/tidy-pandas-load.md b/.changeset/tidy-pandas-load.md
new file mode 100644
index 0000000000..d1332d5c42
--- /dev/null
+++ b/.changeset/tidy-pandas-load.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/start-plugin-core': patch
+---
+
+Preserve exact Vite-resolved module IDs, including virtual prefixes and query variants, when the Start compiler recursively loads imports. Clean IDs only for file-oriented diagnostics and invalidation, and preserve existing query strings when adding compiler-owned lookup flags, so virtual modules such as import-protection mocks reach their plugin load hooks unchanged.
diff --git a/e2e/react-start/import-protection/src/routes/issue-7725.tsx b/e2e/react-start/import-protection/src/routes/issue-7725.tsx
new file mode 100644
index 0000000000..ef0152dd13
--- /dev/null
+++ b/e2e/react-start/import-protection/src/routes/issue-7725.tsx
@@ -0,0 +1,15 @@
+import { createFileRoute } from '@tanstack/react-router'
+import { issue7725ServerFnFactory } from '../violations/issue-7725-server-fn-factory'
+
+const getIssue7725Data = issue7725ServerFnFactory.handler(async () => {
+  return 'issue 7725 server function'
+})
+
+export const Route = createFileRoute('/issue-7725')({
+  loader: () => getIssue7725Data(),
+  component: Issue7725,
+})
+
+function Issue7725() {
+  return <h1>Issue 7725</h1>
+}
diff --git a/e2e/react-start/import-protection/src/violations/issue-7725-server-fn-factory.ts b/e2e/react-start/import-protection/src/violations/issue-7725-server-fn-factory.ts
new file mode 100644
index 0000000000..45be765b1b
--- /dev/null
+++ b/e2e/react-start/import-protection/src/violations/issue-7725-server-fn-factory.ts
@@ -0,0 +1,3 @@
+import { createServerFn } from '@tanstack/react-start'
+
+export const issue7725ServerFnFactory = createServerFn()
diff --git a/e2e/react-start/import-protection/vite.config.ts b/e2e/react-start/import-protection/vite.config.ts
index 3163ded433..6a17f3a7cd 100644
--- a/e2e/react-start/import-protection/vite.config.ts
+++ b/e2e/react-start/import-protection/vite.config.ts
@@ -8,20 +8,43 @@ const outDir = process.env.E2E_DIST_DIR ?? 'dist'
 const startModeConfig = getStartModeConfig()
 const bundledDev = process.env.E2E_VITE_BUNDLED_DEV === 'true'
 
-export default defineConfig({
-  resolve: { tsconfigPaths: true },
-  experimental: bundledDev ? { bundledDev: true } : undefined,
-  build: {
-    outDir,
-  },
-  server: {
-    port: 3000,
-  },
-  plugins: [tanstackStart(startModeConfig), viteReact()],
-  // react-tweet's package.json exports resolve to `index.client.js` which
-  // matches the default **/*.client.* deny pattern.  Bundling it via
-  // noExternal must NOT trigger a false-positive import-protection violation.
-  ssr: {
-    noExternal: ['react-tweet'],
-  },
+const ISSUE_7725_DENIED_SPECIFIER = '../violations/issue-7725-server-fn-factory'
+
+export default defineConfig(({ command }) => {
+  const importProtection =
+    command === 'build'
+      ? {
+          ...startModeConfig.importProtection,
+          client: {
+            // Reproduce build-only issue #7725: resolving this imported
+            // server-fn builder must load import protection's mock virtual
+            // module, including its leading null-byte ID.
+            specifiers: [ISSUE_7725_DENIED_SPECIFIER],
+          },
+        }
+      : startModeConfig.importProtection
+
+  return {
+    resolve: { tsconfigPaths: true },
+    experimental: bundledDev ? { bundledDev: true } : undefined,
+    build: {
+      outDir,
+    },
+    server: {
+      port: 3000,
+    },
+    plugins: [
+      tanstackStart({
+        ...startModeConfig,
+        importProtection,
+      }),
+      viteReact(),
+    ],
+    // react-tweet's package.json exports resolve to `index.client.js` which
+    // matches the default **/*.client.* deny pattern.  Bundling it via
+    // noExternal must NOT trigger a false-positive import-protection violation.
+    ssr: {
+      noExternal: ['react-tweet'],
+    },
+  }
 })
diff --git a/packages/start-plugin-core/src/import-protection/constants.ts b/packages/start-plugin-core/src/import-protection/constants.ts
index 54bb55fdab..4186f6af49 100644
--- a/packages/start-plugin-core/src/import-protection/constants.ts
+++ b/packages/start-plugin-core/src/import-protection/constants.ts
@@ -1,7 +1,3 @@
-import { SERVER_FN_LOOKUP } from '../constants'
-
-export const SERVER_FN_LOOKUP_QUERY = `?${SERVER_FN_LOOKUP}`
-
 export const MOCK_MODULE_ID = 'tanstack-start-import-protection:mock'
 export const MOCK_BUILD_PREFIX = 'tanstack-start-import-protection:mock:build:'
 export const MOCK_EDGE_PREFIX = 'tanstack-start-import-protection:mock-edge:'
diff --git a/packages/start-plugin-core/src/start-compiler/compiler.ts b/packages/start-plugin-core/src/start-compiler/compiler.ts
index d6b36fe6e8..90fd5f564c 100644
--- a/packages/start-plugin-core/src/start-compiler/compiler.ts
+++ b/packages/start-plugin-core/src/start-compiler/compiler.ts
@@ -1537,7 +1537,7 @@ export class StartCompiler {
 
     // TODO improve cycle detection? should we throw here instead of returning 'None'?
     // prevent cycles
-    const vKey = `${cleanId(id)}:${ident}`
+    const vKey = `${id}:${ident}`
     if (visited.has(vKey)) {
       return 'None'
     }
@@ -1634,7 +1634,7 @@ export class StartCompiler {
     resolution: ExportResolution,
     visited = new Set<string>(),
   ): Promise<ExportResolution | undefined> {
-    const key = `${cleanId(resolution.moduleInfo.id)}:${resolution.localName}`
+    const key = `${resolution.moduleInfo.id}:${resolution.localName}`
     if (visited.has(key)) {
       return undefined
     }
@@ -1709,7 +1709,7 @@ export class StartCompiler {
         // Match by resolved binding identity, not by export name alone.
         if (
           target &&
-          cleanId(resolved.moduleInfo.id) === cleanId(target.moduleInfo.id) &&
+          resolved.moduleInfo.id === target.moduleInfo.id &&
           resolved.localName === target.localName
         ) {
           return kind
@@ -1764,7 +1764,7 @@ export class StartCompiler {
 
     // Import aliases can form cycles, e.g. A re-exports from B while B
     // re-exports from A. Track the exported binding before following it.
-    const vKey = `${cleanId(found.moduleInfo.id)}:${found.localName}`
+    const vKey = `${found.moduleInfo.id}:${found.localName}`
     if (visited.has(vKey)) {
       return 'None'
     }
diff --git a/packages/start-plugin-core/src/start-compiler/utils.ts b/packages/start-plugin-core/src/start-compiler/utils.ts
index 36900845fb..384a13113d 100644
--- a/packages/start-plugin-core/src/start-compiler/utils.ts
+++ b/packages/start-plugin-core/src/start-compiler/utils.ts
@@ -25,6 +25,13 @@ export function codeFrameError(
   return new Error(frame)
 }
 
+/**
+ * Converts a bundler module ID to its physical-file identity for diagnostics,
+ * filesystem matching, and file-based invalidation.
+ *
+ * Do not use this for IDs passed to resolve/load hooks or as module cache keys:
+ * virtual prefixes and queries can be part of the module's semantic identity.
+ */
 export function cleanId(id: string): string {
   // Remove null byte prefix used by Vite/Rollup for virtual modules
   if (id.startsWith('\0')) {
diff --git a/packages/start-plugin-core/src/vite/import-protection-plugin/plugin.ts b/packages/start-plugin-core/src/vite/import-protection-plugin/plugin.ts
index 55b98bec73..e319874fc6 100644
--- a/packages/start-plugin-core/src/vite/import-protection-plugin/plugin.ts
+++ b/packages/start-plugin-core/src/vite/import-protection-plugin/plugin.ts
@@ -3,7 +3,8 @@ import { normalizePath } from 'vite'
 import { dirname, relative } from 'pathe'
 
 import { escapeRegExp, resolveViteId } from '../../utils'
-import { VITE_ENVIRONMENT_NAMES } from '../../constants'
+import { SERVER_FN_LOOKUP, VITE_ENVIRONMENT_NAMES } from '../../constants'
+import { hasIdQueryFlag } from '../module-id'
 import {
   ImportGraph,
   buildTrace,
@@ -46,7 +47,6 @@ import { rewriteDeniedImports } from '../../import-protection/rewrite'
 import { ExtensionlessAbsoluteIdResolver } from '../../import-protection/extensionlessAbsoluteIdResolver'
 import {
   IMPORT_PROTECTION_DEBUG,
-  SERVER_FN_LOOKUP_QUERY,
   VITE_BROWSER_VIRTUAL_PREFIX,
 } from '../../import-protection/constants'
 import {
@@ -1013,7 +1013,7 @@ export function importProtectionPlugin(
 
     if (keySet) {
       for (const k of keySet) {
-        if (k.includes(SERVER_FN_LOOKUP_QUERY)) continue
+        if (hasIdQueryFlag(k, SERVER_FN_LOOKUP)) continue
         const imports = env.postTransformImports.get(k)
         if (imports) {
           if (!merged) merged = new Set(imports)
@@ -1051,7 +1051,7 @@ export function importProtectionPlugin(
 
     if (keySet) {
       for (const k of keySet) {
-        if (k.includes(SERVER_FN_LOOKUP_QUERY)) continue
+        if (hasIdQueryFlag(k, SERVER_FN_LOOKUP)) continue
         const imports = env.postTransformImports.get(k)
         if (imports) {
           anyVariantCached = true
@@ -1650,7 +1650,7 @@ export function importProtectionPlugin(
           }
 
           const normalizedImporter = normalizeFilePath(importer)
-          const isDirectLookup = importer.includes(SERVER_FN_LOOKUP_QUERY)
+          const isDirectLookup = hasIdQueryFlag(importer, SERVER_FN_LOOKUP)
           const isBundledClientDev =
             config.command === 'serve' &&
             config.bundledDev &&
@@ -2228,7 +2228,7 @@ export function importProtectionPlugin(
           const cacheKey = normalizePath(id)
 
           const envState = getEnv(envName)
-          const isServerFnLookup = id.includes(SERVER_FN_LOOKUP_QUERY)
+          const isServerFnLookup = hasIdQueryFlag(id, SERVER_FN_LOOKUP)
 
           // Propagate SERVER_FN_LOOKUP status before import-analysis
           if (isServerFnLookup) {
diff --git a/packages/start-plugin-core/src/vite/module-id.ts b/packages/start-plugin-core/src/vite/module-id.ts
new file mode 100644
index 0000000000..ef2ad98f10
--- /dev/null
+++ b/packages/start-plugin-core/src/vite/module-id.ts
@@ -0,0 +1,31 @@
+/** Checks for a query parameter without rewriting the opaque module ID. */
+export function hasIdQueryFlag(id: string, flag: string): boolean {
+  const queryIndex = id.indexOf('?')
+  if (queryIndex === -1) {
+    return false
+  }
+
+  return new URLSearchParams(id.slice(queryIndex + 1)).has(flag)
+}
+
+/** Appends an owned query flag without normalizing the existing query. */
+export function appendIdQueryFlag(id: string, flag: string): string {
+  if (!id.includes('?')) {
+    return `${id}?${flag}`
+  }
+
+  const separator = id.endsWith('&') ? '' : '&'
+  return `${id}${separator}${flag}`
+}
+
+/** Removes the owned query flag appended by {@link appendIdQueryFlag}. */
+export function removeIdQueryFlag(id: string, flag: string): string {
+  for (const separator of ['?', '&']) {
+    const suffix = `${separator}${flag}`
+    if (id.endsWith(suffix)) {
+      return id.slice(0, -suffix.length)
+    }
+  }
+
+  return id
+}
diff --git a/packages/start-plugin-core/src/vite/start-compiler-plugin/plugin.ts b/packages/start-plugin-core/src/vite/start-compiler-plugin/plugin.ts
index 6309b76eb2..1cc02f3b91 100644
--- a/packages/start-plugin-core/src/vite/start-compiler-plugin/plugin.ts
+++ b/packages/start-plugin-core/src/vite/start-compiler-plugin/plugin.ts
@@ -21,6 +21,7 @@ import {
   createHydrateCompilerPlugin,
 } from '../../hydrate-when-transform'
 import { resolveViteId } from '../../utils'
+import { appendIdQueryFlag, removeIdQueryFlag } from '../module-id'
 import {
   createViteDevServerFnModuleSpecifierEncoder,
   decodeViteDevServerModuleSpecifier,
@@ -351,7 +352,7 @@ export function startCompilerPlugin(
                   {
                     load: (options) => this.load(options),
                     error: (message) => this.error(message),
-                    devId: `${id}?${SERVER_FN_LOOKUP}`,
+                    devId: appendIdQueryFlag(id, SERVER_FN_LOOKUP),
                   },
                 )
                 if (code !== undefined) {
@@ -364,7 +365,10 @@ export function startCompilerPlugin(
 
                 if (r) {
                   if (!r.external) {
-                    return cleanId(r.id)
+                    // Keep the resolved ID intact because it is passed back to
+                    // Vite's load hook. Virtual-module prefixes and queries are
+                    // part of that load identity, not compiler-only metadata.
+                    return r.id
                   }
                 }
 
@@ -496,7 +500,10 @@ export function startCompilerPlugin(
         },
         handler(code, id) {
           const compiler = compilers.get(this.environment.name)
-          compiler?.ingestModule({ code, id: cleanId(id) })
+          compiler?.ingestModule({
+            code,
+            id: removeIdQueryFlag(id, SERVER_FN_LOOKUP),
+          })
         },
       },
     },
diff --git a/packages/start-plugin-core/tests/createServerFn/createServerFn.test.ts b/packages/start-plugin-core/tests/createServerFn/createServerFn.test.ts
index c4009657c4..230caf7173 100644
--- a/packages/start-plugin-core/tests/createServerFn/createServerFn.test.ts
+++ b/packages/start-plugin-core/tests/createServerFn/createServerFn.test.ts
@@ -457,6 +457,64 @@ describe('createServerFn compiles correctly', async () => {
     )
   })
 
+  test('keeps query-bearing virtual module identities distinct', async () => {
+    const publicFactoryId = '\0virtual:server-fn-factory?variant=public'
+    const implementationFactoryId =
+      '\0virtual:server-fn-factory?variant=implementation'
+    const virtualModules: Record<string, string> = {
+      [publicFactoryId]: `
+        import { createIssueServerFn } from 'virtual:server-fn-factory?variant=implementation'
+        export { createIssueServerFn }
+      `,
+      [implementationFactoryId]: `
+        import { createServerFn } from '@tanstack/react-start'
+        export const createIssueServerFn = createServerFn
+      `,
+    }
+    const loadedIds: Array<string> = []
+
+    const compiler = new StartCompiler({
+      env: 'client',
+      ...getDefaultTestOptions('client'),
+      mode: 'build',
+      loadModule: async (id) => {
+        loadedIds.push(id)
+        const code = virtualModules[id]
+        if (code) {
+          compiler.ingestModule({ code, id })
+        }
+      },
+      lookupKinds: new Set(['ServerFn']),
+      lookupConfigurations: [
+        {
+          libName: '@tanstack/react-start',
+          rootExport: 'createServerFn',
+          kind: 'Root',
+        },
+      ],
+      getKnownServerFns: () => ({}),
+      resolveId: async (source) => {
+        if (source.startsWith('virtual:server-fn-factory?')) {
+          return `\0${source}`
+        }
+
+        return null
+      },
+    })
+
+    const result = await compiler.compile({
+      id: '/test/src/test.ts',
+      code: `
+        import { createIssueServerFn } from 'virtual:server-fn-factory?variant=public'
+        const issueServerFn = createIssueServerFn().handler(async () => 'ok')
+      `,
+    })
+
+    expect(result).not.toBeNull()
+    expect(result!.code).toContain('createClientRpc')
+    expect(loadedIds).toEqual([publicFactoryId, implementationFactoryId])
+  })
+
   test('should resolve local named re-exports of createServerFn', async () => {
     const code = `
       import { createFooServerFn } from './factory'
diff --git a/packages/start-plugin-core/tests/vite/module-id.test.ts b/packages/start-plugin-core/tests/vite/module-id.test.ts
new file mode 100644
index 0000000000..003926a606
--- /dev/null
+++ b/packages/start-plugin-core/tests/vite/module-id.test.ts
@@ -0,0 +1,56 @@
+import { describe, expect, test } from 'vitest'
+import {
+  appendIdQueryFlag,
+  hasIdQueryFlag,
+  removeIdQueryFlag,
+} from '../../src/vite/module-id'
+
+const flag = 'server-fn-module-lookup'
+
+describe('hasIdQueryFlag', () => {
+  test.each([
+    ['/src/route.ts', false],
+    [`/src/route.ts?${flag}`, true],
+    [`/src/route.ts?mode=dev&${flag}`, true],
+    [`/src/route.ts?${flag}=enabled`, true],
+    [`/src/route.ts?mode=${flag}`, false],
+    [`/src/route.ts?${flag}-suffix`, false],
+  ])('checks the query parameter name in %s', (id, expected) => {
+    expect(hasIdQueryFlag(id, flag)).toBe(expected)
+  })
+})
+
+describe('appendIdQueryFlag', () => {
+  test.each([
+    ['/src/route.ts', `/src/route.ts?${flag}`],
+    ['/src/route.ts?mode=dev', `/src/route.ts?mode=dev&${flag}`],
+    ['/src/route.ts?', `/src/route.ts?&${flag}`],
+    ['/src/route.ts?mode=dev&', `/src/route.ts?mode=dev&${flag}`],
+  ])('appends the flag to %s', (id, expected) => {
+    expect(appendIdQueryFlag(id, flag)).toBe(expected)
+  })
+})
+
+describe('removeIdQueryFlag', () => {
+  test.each([
+    [`/src/route.ts?${flag}`, '/src/route.ts'],
+    [`/src/route.ts?mode=dev&${flag}`, '/src/route.ts?mode=dev'],
+    [`/src/route.ts?${flag}&mode=dev`, `/src/route.ts?${flag}&mode=dev`],
+    ['/src/route.ts?mode=dev', '/src/route.ts?mode=dev'],
+  ])('removes only an appended flag from %s', (id, expected) => {
+    expect(removeIdQueryFlag(id, flag)).toBe(expected)
+  })
+})
+
+describe('module ID query flag round trip', () => {
+  test.each([
+    '/src/route.ts',
+    '/src/route.ts?',
+    '/src/route.ts?variant=client',
+    '\0virtual:factory?variant=client&encoded=a%2Fb',
+    `/src/route.ts?${flag}`,
+  ])('preserves the original ID %s', (id) => {
+    const withFlag = appendIdQueryFlag(id, flag)
+    expect(removeIdQueryFlag(withFlag, flag)).toBe(id)
+  })
+})