diff --git a/bin/gstack-team-init b/bin/gstack-team-init
index 2687f7d73..a416d40fa 100755
--- a/bin/gstack-team-init
+++ b/bin/gstack-team-init
@@ -215,6 +215,13 @@ HOOK_EOF
     " 2>/dev/null
     GENERATED+=(".claude/settings.json")
     echo "  + .claude/settings.json — PreToolUse hook registered"
+
+    # Remove the obsolete Bash hook only after its replacement is generated and
+    # registered successfully. Other project hooks are left untouched.
+    if [ -e "$HOOKS_DIR/check-gstack.sh" ] || [ -L "$HOOKS_DIR/check-gstack.sh" ]; then
+      rm "$HOOKS_DIR/check-gstack.sh"
+      echo "  - .claude/hooks/check-gstack.sh — removed legacy enforcement hook"
+    fi
   else
     echo "  ! bun not found — manually add the PreToolUse hook to .claude/settings.json"
   fi
diff --git a/implementation-notes.html b/implementation-notes.html
index c2d307d35..d4e2fad0f 100644
--- a/implementation-notes.html
+++ b/implementation-notes.html
@@ -18,7 +18,7 @@
       <li>The generated hook resolves the user home in <code>HOME</code>, <code>USERPROFILE</code>, then <code>os.homedir()</code> order so POSIX, Git Bash, PowerShell, and cmd runners use the expected global install root.</li>
       <li>The hook contract follows <code>docs/spikes/claude-code-hook-mutation.md</code>: pass-through writes <code>{}</code>; denial writes a <code>hookSpecificOutput</code> object for <code>PreToolUse</code> with <code>permissionDecision: "deny"</code>.</li>
       <li>Missing or unreadable gstack is an intentional denial with exit code zero. Install instructions are present in stderr and <code>permissionDecisionReason</code>, so the runner does not report a hook execution error.</li>
-      <li>Rerunning required mode replaces a matching legacy <code>check-gstack.sh</code> registration and removes duplicate matching registrations.</li>
+      <li>Rerunning required mode replaces a matching legacy <code>check-gstack.sh</code> registration, removes duplicate matching registrations, and deletes the obsolete Bash hook only after the CommonJS hook is generated and registered successfully. Unrelated project hooks remain unchanged.</li>
     </ul>
 
     <h2>Deviations</h2>
diff --git a/test/team-mode.test.ts b/test/team-mode.test.ts
index e3101a3ec..b555f471c 100644
--- a/test/team-mode.test.ts
+++ b/test/team-mode.test.ts
@@ -397,7 +397,7 @@ describe('gstack-team-init', () => {
     });
 
     expectStructuredDeny(result, MISSING_PROJECT_REASON);
-  });
+  }, 30_000);
 
   test('required: stale project paths deny through the platform default shell', () => {
     run(`${TEAM_INIT} required`, { cwd: tmpDir });
@@ -445,7 +445,7 @@ describe('gstack-team-init', () => {
       expectStructuredDeny(result, HOOK_LOAD_REASON);
       expect(result.stderr).not.toContain(projectDir);
     }
-  });
+  }, 30_000);
 
   test('required: hook runs in PowerShell with USERPROFILE home fallback', () => {
     if (process.platform !== 'win32') return;
@@ -472,7 +472,7 @@ describe('gstack-team-init', () => {
     expect(result.exitCode).toBe(0);
     expect(result.stderr).toBe('');
     expect(JSON.parse(result.stdout)).toEqual({});
-  });
+  }, 30_000);
 
   test('required: missing gstack returns an intentional deny, not a hook error', () => {
     run(`${TEAM_INIT} required`, { cwd: tmpDir });
@@ -507,10 +507,14 @@ describe('gstack-team-init', () => {
     });
   });
 
-  test('required: rerun upgrades a legacy Bash hook without duplicates', () => {
+  test('required: rerun removes a legacy Bash hook without touching other hooks', () => {
     const hooksDir = path.join(tmpDir, '.claude', 'hooks');
+    const legacyHook = path.join(hooksDir, 'check-gstack.sh');
+    const unrelatedHook = path.join(hooksDir, 'check-project.cjs');
+    const unrelatedHookContents = "console.log('project hook');\n";
     fs.mkdirSync(hooksDir, { recursive: true });
-    fs.writeFileSync(path.join(hooksDir, 'check-gstack.sh'), '#!/bin/bash\n');
+    fs.writeFileSync(legacyHook, '#!/bin/bash\n');
+    fs.writeFileSync(unrelatedHook, unrelatedHookContents);
     fs.writeFileSync(
       path.join(tmpDir, '.claude', 'settings.json'),
       JSON.stringify({
@@ -527,17 +531,31 @@ describe('gstack-team-init', () => {
         },
       }),
     );
+    execSync('git add .claude', { cwd: tmpDir });
+    execSync('git commit -m "add legacy hook"', { cwd: tmpDir });
+
+    run(`${TEAM_INIT} required`, { cwd: tmpDir });
+    expect(fs.existsSync(legacyHook)).toBe(false);
+    expect(fs.readFileSync(unrelatedHook, 'utf-8')).toBe(unrelatedHookContents);
 
     run(`${TEAM_INIT} required`, { cwd: tmpDir });
     const settings = JSON.parse(
       fs.readFileSync(path.join(tmpDir, '.claude', 'settings.json'), 'utf-8'),
     );
+    expect(fs.existsSync(legacyHook)).toBe(false);
+    expect(fs.readFileSync(unrelatedHook, 'utf-8')).toBe(unrelatedHookContents);
+    expect(
+      execSync('git status --short -- .claude/hooks/check-gstack.sh', {
+        cwd: tmpDir,
+        encoding: 'utf-8',
+      }),
+    ).toBe(' D .claude/hooks/check-gstack.sh\n');
     expect(settings.hooks.PreToolUse).toHaveLength(1);
     expect(settings.hooks.PreToolUse[0].hooks).toHaveLength(1);
     expect(settings.hooks.PreToolUse[0].hooks[0].command).toContain(
       'check-gstack.cjs',
     );
-  });
+  }, 30_000);
 
   test('idempotent: running twice does not duplicate CLAUDE.md section', () => {
     run(`${TEAM_INIT} optional`, { cwd: tmpDir });