diff --git a/skills/workos-authkit-tanstack-start/SKILL.md b/skills/workos-authkit-tanstack-start/SKILL.md
index c83ed2d..36356de 100644
--- a/skills/workos-authkit-tanstack-start/SKILL.md
+++ b/skills/workos-authkit-tanstack-start/SKILL.md
@@ -86,6 +86,8 @@ Default redirect URI: `http://localhost:3000/api/auth/callback`
 
 **authkitMiddleware MUST be configured or auth will fail silently.**
 
+**WARNING: Do NOT add middleware to `createRouter()` in `router.tsx` or `app.tsx`. That is TanStack Router (client-side only). Server middleware belongs in `start.ts` using `requestMiddleware`.**
+
 Create or update `src/start.ts` (or `app/start.ts` for legacy):
 
 ```typescript
diff --git a/src/doctor/checks/auth-patterns.spec.ts b/src/doctor/checks/auth-patterns.spec.ts
index 0226bda..0617360 100644
--- a/src/doctor/checks/auth-patterns.spec.ts
+++ b/src/doctor/checks/auth-patterns.spec.ts
@@ -368,7 +368,7 @@ describe('checkAuthPatterns', () => {
       expect(result.findings.find((f) => f.code === 'CALLBACK_ROUTE_MISSING')).toBeUndefined();
     });
 
-    it('no finding when callback route exists (TanStack Start flat)', async () => {
+    it('no finding when callback route exists (TanStack Start flat in src/)', async () => {
       writeFixtureFile(
         testDir,
         'src/routes/auth.callback.tsx',
@@ -382,6 +382,36 @@ describe('checkAuthPatterns', () => {
       );
       expect(result.findings.find((f) => f.code === 'CALLBACK_ROUTE_MISSING')).toBeUndefined();
     });
+
+    it('no finding when callback route exists (TanStack Start nested in src/)', async () => {
+      writeFixtureFile(
+        testDir,
+        'src/routes/api/auth/callback.tsx',
+        'export const Route = createFileRoute("/api/auth/callback")',
+      );
+      const result = await checkAuthPatterns(
+        makeOptions(testDir),
+        makeFramework({ name: 'TanStack Start', version: '1.0.0', expectedCallbackPath: '/api/auth/callback' }),
+        makeEnv(),
+        makeSdk({ name: '@workos-inc/authkit-tanstack-start' }),
+      );
+      expect(result.findings.find((f) => f.code === 'CALLBACK_ROUTE_MISSING')).toBeUndefined();
+    });
+
+    it('no finding when callback route exists (TanStack Start flat in app/)', async () => {
+      writeFixtureFile(
+        testDir,
+        'app/routes/api.auth.callback.tsx',
+        'export const Route = createFileRoute("/api/auth/callback")',
+      );
+      const result = await checkAuthPatterns(
+        makeOptions(testDir),
+        makeFramework({ name: 'TanStack Start', version: '1.0.0', expectedCallbackPath: '/api/auth/callback' }),
+        makeEnv(),
+        makeSdk({ name: '@workos-inc/authkit-tanstack-start' }),
+      );
+      expect(result.findings.find((f) => f.code === 'CALLBACK_ROUTE_MISSING')).toBeUndefined();
+    });
   });
 
   describe('API_KEY_LEAKED_TO_CLIENT', () => {
@@ -514,7 +544,7 @@ describe('checkAuthPatterns', () => {
 
   describe('MISSING_AUTHKIT_MIDDLEWARE (TanStack Start)', () => {
     it('warning when start.ts lacks authkitMiddleware', async () => {
-      writeFixtureFile(testDir, 'src/start.ts', 'export default defineStart({})');
+      writeFixtureFile(testDir, 'src/start.ts', 'export default createStart({})');
       const result = await checkAuthPatterns(
         makeOptions(testDir),
         makeFramework({ name: 'TanStack Start', expectedCallbackPath: '/auth/callback' }),
@@ -529,8 +559,9 @@ describe('checkAuthPatterns', () => {
         testDir,
         'src/start.ts',
         `
+        import { createStart } from "@tanstack/react-start";
         import { authkitMiddleware } from "@workos-inc/authkit-tanstack-start";
-        export default defineStart({ middleware: [authkitMiddleware()] });
+        export default createStart({ requestMiddleware: [authkitMiddleware()] });
       `,
       );
       const result = await checkAuthPatterns(
diff --git a/src/doctor/checks/auth-patterns.ts b/src/doctor/checks/auth-patterns.ts
index 15af4a0..fbfd8f2 100644
--- a/src/doctor/checks/auth-patterns.ts
+++ b/src/doctor/checks/auth-patterns.ts
@@ -299,13 +299,16 @@ function checkCallbackRouteMissing(ctx: CheckContext): AuthPatternFinding[] {
       possiblePaths.push(join(ctx.installDir, 'app', 'routes', nested + `.${ext}`));
     }
   } else if (ctx.framework.name === 'TanStack Start') {
-    // Modern flat: src/routes/api.auth.callback.tsx  Legacy nested: app/routes/api/auth/callback.tsx
+    // Flat: routes/api.auth.callback.tsx  Nested: routes/api/auth/callback.tsx
+    // Both conventions work in both src/ and app/ directories
     const segments = callbackPath.replace(/^\//, '').split('/');
     const flat = segments.join('.');
     const nested = segments.join('/');
-    for (const ext of ['tsx', 'jsx', 'ts', 'js']) {
-      possiblePaths.push(join(ctx.installDir, 'src', 'routes', `${flat}.${ext}`));
-      possiblePaths.push(join(ctx.installDir, 'app', 'routes', nested + `.${ext}`));
+    for (const prefix of ['src', 'app']) {
+      for (const ext of ['tsx', 'jsx', 'ts', 'js']) {
+        possiblePaths.push(join(ctx.installDir, prefix, 'routes', `${flat}.${ext}`));
+        possiblePaths.push(join(ctx.installDir, prefix, 'routes', nested + `.${ext}`));
+      }
     }
   }
 
@@ -423,7 +426,10 @@ function checkMissingAuthkitMiddleware(ctx: CheckContext): AuthPatternFinding[]
       severity: 'warning',
       message: 'start.ts does not reference authkitMiddleware — AuthKit session handling requires it',
       filePath: relative(ctx.installDir, startFile),
-      remediation: 'Add authkitMiddleware to your start.ts server middleware configuration.',
+      remediation:
+        'Add authkitMiddleware to requestMiddleware in src/start.ts:\n' +
+        '  import { authkitMiddleware } from "@workos/authkit-tanstack-react-start";\n' +
+        '  export default createStart({ requestMiddleware: [authkitMiddleware()] });',
     },
   ];
 }