diff --git a/src/__tests__/doctor.test.ts b/src/__tests__/doctor.test.ts
index a93e05cfc..cd1978a7d 100644
--- a/src/__tests__/doctor.test.ts
+++ b/src/__tests__/doctor.test.ts
@@ -286,6 +286,43 @@ describe('doctor — hook checks', () => {
         expect(allPassed).toBe(false);
     });
 
+    // Non-self project scope: `hooks inject` writes copilot at
+    // <projectRoot>/.github/hooks/teamai.json (the config's own scope), so doctor
+    // must probe that file — not userScope.hooks joined onto projectRoot.
+    it('checks project Copilot hooks where inject wrote them when userScope.hooks is set', async () => {
+        const projectRoot = '/tmp/teamai-doctor-copilot-project-userscope';
+        const hookPath = path.join(projectRoot, '.github', 'hooks', 'teamai.json');
+        mockedLoadLocalConfig.mockResolvedValue({
+            ...mockLocalConfig,
+            scope: 'project',
+            projectRoot,
+            enabledAgents: ['copilot'],
+        });
+        mockedLoadTeamConfig.mockResolvedValue({
+            ...mockTeamConfig,
+            sharing: { env: { injectShellProfile: false } },
+            toolPaths: {
+                copilot: {
+                    hooks: '.github/hooks/teamai.json',
+                    userScope: { hooks: 'hooks/teamai.json' },
+                },
+            },
+        });
+        mockedPathExists.mockImplementation(async (filePath: string) => (
+            filePath === hookPath || filePath === path.dirname(hookPath)
+        ));
+        mockedReadFileSafe.mockImplementation(async (filePath: string) => (
+            filePath === hookPath ? buildFullHooksContent() : null
+        ));
+
+        await doctor({});
+        const copilotLine = consoleSpy.mock.calls
+            .map((call) => String(call[0]))
+            .find((message) => message.includes('hooks in copilot'));
+
+        expect(copilotLine).toContain('✔');
+    });
+
     it('does not infer project Copilot installation from .github/hooks alone', async () => {
         const projectRoot = '/tmp/teamai-doctor-unselected-copilot';
         const copilotHome = '/tmp/teamai-doctor-unselected-home';
diff --git a/src/doctor.ts b/src/doctor.ts
index b403ca65a..91ae901c4 100644
--- a/src/doctor.ts
+++ b/src/doctor.ts
@@ -170,15 +170,23 @@ async function buildEnabledToolChecks(ctx: DoctorContext): Promise<Check[]> {
  */
 async function buildHookChecks(
   toolPaths: TeamaiConfig['toolPaths'],
+  hookToolPaths: TeamaiConfig['toolPaths'],
   baseDir: string,
   localConfig: LocalConfig,
 ): Promise<Check[]> {
   const checks: Check[] = [];
   for (const [tool, paths] of Object.entries(toolPaths)) {
+    // A standalone hooks file (Copilot) is injected at the config's own scope
+    // (`reconcileTeamHooksForConfig` joins resolveToolBaseDir with the
+    // config-scoped `hooks`), so it is probed from `toolPaths`. Settings-based
+    // hooks follow resolveHookScope and are probed from `hookToolPaths`.
+    // Mixing the two — userScope `hooks/teamai.json` under <projectRoot> —
+    // reported Copilot missing right after a successful `hooks inject` (#732).
+    const settings = hookToolPaths[tool]?.settings;
     const hookPath = paths.hooks
       ? path.join(resolveToolBaseDir(tool, localConfig), paths.hooks)
-      : paths.settings
-        ? path.join(baseDir, paths.settings)
+      : settings
+        ? path.join(baseDir, settings)
         : undefined;
     if (!hookPath) continue;
     const settingsPath = hookPath;
@@ -375,7 +383,7 @@ export async function buildChecks(ctx: DoctorContext, stage: CheckStage = 'docto
         + 'can push to the team repo (run with --verbose to see the push error).',
     },
     ...await buildEnabledToolChecks(ctx),
-    ...await buildHookChecks(hookToolPaths, baseDir, localConfig),
+    ...await buildHookChecks(toolPaths, hookToolPaths, baseDir, localConfig),
     ...await buildDeliveryChecks(ctx),
     // Built only for `doctor`: the work is in building these, not in running
     // them, so skipping them post-pull is what keeps the budget for the rest.