diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1f7dddf..0ca8eb9 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -86,7 +86,11 @@ jobs:
           npm link angular-cli-ghpages
           npx ng add angular-cli-ghpages
           npx ng deploy
+          echo second > dist/test-app-18/browser/second.txt
+          npx ng deploy --no-build --message="second deploy"
           cd /tmp/remote-18.git && git branch | grep gh-pages
+          test "$(git rev-list --count gh-pages)" = 2
+          git cat-file -e gh-pages:.nojekyll
           echo "Angular 18: build + deploy successful"
 
       - name: Test Angular 19
@@ -99,7 +103,11 @@ jobs:
           npm link angular-cli-ghpages
           npx ng add angular-cli-ghpages
           npx ng deploy
+          echo second > dist/test-app-19/browser/second.txt
+          npx ng deploy --no-build --message="second deploy"
           cd /tmp/remote-19.git && git branch | grep gh-pages
+          test "$(git rev-list --count gh-pages)" = 2
+          git cat-file -e gh-pages:.nojekyll
           echo "Angular 19: build + deploy successful"
 
       - name: Test Angular 20
@@ -112,7 +120,11 @@ jobs:
           npm link angular-cli-ghpages
           npx ng add angular-cli-ghpages
           npx ng deploy
+          echo second > dist/test-app-20/browser/second.txt
+          npx ng deploy --no-build --message="second deploy"
           cd /tmp/remote-20.git && git branch | grep gh-pages
+          test "$(git rev-list --count gh-pages)" = 2
+          git cat-file -e gh-pages:.nojekyll
           echo "Angular 20: build + deploy successful"
 
       - name: Test Angular 21
@@ -125,7 +137,11 @@ jobs:
           npm link angular-cli-ghpages
           npx ng add angular-cli-ghpages
           npx ng deploy
+          echo second > dist/test-app-21/browser/second.txt
+          npx ng deploy --no-build --message="second deploy"
           cd /tmp/remote-21.git && git branch | grep gh-pages
+          test "$(git rev-list --count gh-pages)" = 2
+          git cat-file -e gh-pages:.nojekyll
           echo "Angular 21: build + deploy successful"
 
       - name: Test Angular 22
@@ -138,5 +154,9 @@ jobs:
           npm link angular-cli-ghpages
           npx ng add angular-cli-ghpages
           npx ng deploy
+          echo second > dist/test-app-22/browser/second.txt
+          npx ng deploy --no-build --message="second deploy"
           cd /tmp/remote-22.git && git branch | grep gh-pages
+          test "$(git rev-list --count gh-pages)" = 2
+          git cat-file -e gh-pages:.nojekyll
           echo "Angular 22: build + deploy successful"
diff --git a/src/engine/engine.gh-pages-cleanup.spec.ts b/src/engine/engine.gh-pages-cleanup.spec.ts
index c734023..d355162 100644
--- a/src/engine/engine.gh-pages-cleanup.spec.ts
+++ b/src/engine/engine.gh-pages-cleanup.spec.ts
@@ -153,6 +153,62 @@ describe('end-to-end cleanup regression (issue #204, real git)', () => {
     expect(tree).not.toContain('stale.html');
   }, 30_000);
 
+  it('keeps .nojekyll and CNAME on a redeploy', async () => {
+    const deploy = () => engine.run(
+      distDir,
+      {
+        repo: bareRepoPath,
+        branch: 'gh-pages',
+        dotfiles: true,
+        notfound: false,
+        nojekyll: true,
+        cname: 'example.org',
+        name: 'Test',
+        email: 'test@test.com',
+        message: 'test deploy'
+      },
+      new logging.NullLogger()
+    );
+
+    await deploy();
+    await fs.writeFile(path.join(distDir, 'index.html'), '<html>second deploy</html>\n');
+    await deploy();
+
+    const tree = git('ls-tree -r gh-pages --name-only', { cwd: bareRepoPath })
+      .split('\n')
+      .filter(Boolean)
+      .sort();
+
+    expect(tree).toEqual(['.nojekyll', 'CNAME', 'index.html']);
+    expect(git('show gh-pages:CNAME', { cwd: bareRepoPath })).toBe('example.org');
+  }, 30_000);
+
+  it('removes a leftover .nojekyll when nojekyll is disabled', async () => {
+    const deploy = (nojekyll: boolean) => engine.run(
+      distDir,
+      {
+        repo: bareRepoPath,
+        branch: 'gh-pages',
+        dotfiles: true,
+        notfound: false,
+        nojekyll,
+        name: 'Test',
+        email: 'test@test.com',
+        message: 'test deploy'
+      },
+      new logging.NullLogger()
+    );
+
+    await deploy(true);
+    await deploy(false);
+
+    const tree = git('ls-tree -r gh-pages --name-only', { cwd: bareRepoPath })
+      .split('\n')
+      .filter(Boolean);
+
+    expect(tree).toEqual(['index.html']);
+  }, 30_000);
+
   it('baseline: without our hook, gh-pages alone leaks dotfiles and submodule gitlinks (demonstrates the upstream bug)', async () => {
     // Call gh-pages.publish() directly — no engine.run(), no beforeAdd hook.
     // This is exactly what angular-cli-ghpages v3 did before our fix.
diff --git a/src/engine/engine.prepare-options-helpers.spec.ts b/src/engine/engine.prepare-options-helpers.spec.ts
index a876d6d..444c75a 100644
--- a/src/engine/engine.prepare-options-helpers.spec.ts
+++ b/src/engine/engine.prepare-options-helpers.spec.ts
@@ -721,4 +721,47 @@ describe('prepareOptions helpers - intensive tests', () => {
       }
     });
   });
+
+  describe('createCleanupBeforeAddHook', () => {
+    let distDir: string;
+
+    beforeEach(async () => {
+      distDir = await fs.mkdtemp(path.join(os.tmpdir(), 'ghp-hook-'));
+      await fs.writeFile(path.join(distDir, 'index.html'), '<html></html>');
+    });
+
+    afterEach(async () => {
+      await fs.rm(distDir, { recursive: true, force: true });
+    });
+
+    function createGit(tracked: string[]) {
+      const git: helpers.GhPagesGit = {
+        cwd: '/clone',
+        output: '',
+        exec: vi.fn(async () => {
+          git.output = tracked.join('\0');
+          return git;
+        }),
+        rm: vi.fn(async () => git)
+      };
+      return git;
+    }
+
+    it('keeps generated files that are tracked but not in dist', async () => {
+      const git = createGit(['.nojekyll', 'CNAME', 'index.html']);
+      const generatedFiles = ['.nojekyll', 'CNAME'];
+
+      await helpers.createCleanupBeforeAddHook(distDir, true, testLogger, generatedFiles)(git);
+
+      expect(git.rm).not.toHaveBeenCalled();
+    });
+
+    it('removes tracked files that are neither in dist nor generated', async () => {
+      const git = createGit(['.nojekyll', 'index.html', 'stale.html']);
+
+      await helpers.createCleanupBeforeAddHook(distDir, true, testLogger, [])(git);
+
+      expect(git.rm).toHaveBeenCalledWith(['.nojekyll', 'stale.html']);
+    });
+  });
 });
diff --git a/src/engine/engine.prepare-options-helpers.ts b/src/engine/engine.prepare-options-helpers.ts
index 46c8910..793d357 100644
--- a/src/engine/engine.prepare-options-helpers.ts
+++ b/src/engine/engine.prepare-options-helpers.ts
@@ -346,6 +346,10 @@ export async function collectDistFiles(
  * indexed (`git ls-files -z`), diff against the set of files in our dist, and
  * `git rm` the leftovers. `git rm` correctly handles submodule gitlinks too.
  *
+ * `generatedFiles` lists files that gh-pages itself writes into the clone
+ * (`.nojekyll`, `CNAME`). They never exist in dist, so they are kept explicitly;
+ * otherwise a redeploy would remove the `.nojekyll` that gh-pages just created.
+ *
  * Upstream fix: tschaub/gh-pages#612 (merged 2025-08-09, unreleased as of
  * gh-pages@6.3.0). When a release containing that PR lands, this hook becomes
  * redundant and can be removed.
@@ -353,13 +357,14 @@ export async function collectDistFiles(
 export function createCleanupBeforeAddHook(
   distDir: string,
   dotfiles: boolean,
-  logger: logging.LoggerApi
+  logger: logging.LoggerApi,
+  generatedFiles: string[]
 ): (git: GhPagesGit) => Promise<void> {
   return async (git) => {
     const distFiles = await collectDistFiles(distDir, dotfiles);
     await git.exec('ls-files', '-z');
     const tracked = (git.output || '').split('\0').filter(Boolean);
-    const toRemove = tracked.filter((f) => !distFiles.has(f));
+    const toRemove = tracked.filter((f) => !distFiles.has(f) && !generatedFiles.includes(f));
     if (toRemove.length === 0) {
       return;
     }
diff --git a/src/engine/engine.ts b/src/engine/engine.ts
index 4fde957..67f8d57 100644
--- a/src/engine/engine.ts
+++ b/src/engine/engine.ts
@@ -49,7 +49,7 @@ export async function run(
 
   await checkIfDistFolderExists(dir);
   await createNotFoundFile(dir, prepared, logger);
-  // Note: CNAME and .nojekyll files are now created by gh-pages v6+ via options
+  // gh-pages writes CNAME and .nojekyll into its clone (cname/nojekyll options)
   await publishViaGhPages(ghpages, dir, prepared, logger);
 
   if (!prepared.dryRun) {
@@ -150,8 +150,21 @@ async function createNotFoundFile(
   }
 }
 
-// CNAME and .nojekyll files are now handled by gh-pages v6+ via the cname/nojekyll options
-// Previously we created these files ourselves before publishing, but gh-pages PR #533 added native support
+/**
+ * Files that gh-pages writes into its clone (not into dist) for the given options.
+ * gh-pages' own remove step already unstages CNAME before rewriting it; listing it
+ * here keeps the cleanup hook correct independently of that detail.
+ */
+function generatedFiles(options: PreparedOptions): string[] {
+  const files: string[] = [];
+  if (options.nojekyll) {
+    files.push('.nojekyll');
+  }
+  if (options.cname) {
+    files.push('CNAME');
+  }
+  return files;
+}
 
 async function publishViaGhPages(
   ghPages: GHPages,
@@ -206,7 +219,7 @@ async function publishViaGhPages(
     // Workaround for gh-pages#612 (unreleased in v6.3.0): clean up leftover
     // gh-pages branch files (dotfiles, submodule gitlinks) that the broken
     // remove step misses. Skipped when the user opts into additive mode.
-    beforeAdd: options.add ? undefined : createCleanupBeforeAddHook(dir, options.dotfiles, logger)
+    beforeAdd: options.add ? undefined : createCleanupBeforeAddHook(dir, options.dotfiles, logger, generatedFiles(options))
   };
 
   // gh-pages@6 silently absorbs errors via its internal .then(_, onRejected)
diff --git a/src/package-lock.json b/src/package-lock.json
index 8e6d7e9..f1c6656 100644
--- a/src/package-lock.json
+++ b/src/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "angular-cli-ghpages",
-  "version": "3.1.1",
+  "version": "3.1.2",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "angular-cli-ghpages",
-      "version": "3.1.1",
+      "version": "3.1.2",
       "license": "MIT",
       "dependencies": {
         "@angular-devkit/architect": ">=0.1800.0 <0.2300.0",
diff --git a/src/package.json b/src/package.json
index 8662572..ff12760 100644
--- a/src/package.json
+++ b/src/package.json
@@ -1,6 +1,6 @@
 {
   "name": "angular-cli-ghpages",
-  "version": "3.1.1",
+  "version": "3.1.2",
   "description": "Deploy your Angular app to GitHub Pages or Cloudflare Pages directly from the Angular CLI (ng deploy)",
   "main": "index.js",
   "types": "index.d.ts",