diff --git a/fdroidserver/checkupdates.py b/fdroidserver/checkupdates.py
index d158e1d6..f75e96da 100644
--- a/fdroidserver/checkupdates.py
+++ b/fdroidserver/checkupdates.py
@@ -724,6 +724,27 @@ def push_commits(remote_name='origin'):
                 logging.debug(remote.url + ': ' + pushinfo.summary)
 
 
+def prune_empty_appid_branches(git_repo=None):
+    """Remove empty branches from checkupdates-bot git remote."""
+    if git_repo is None:
+        git_repo = git.Repo.init('.')
+    main_branch = 'main'
+    if main_branch not in git_repo.remotes.upstream.refs:
+        main_branch = 'master'
+    upstream_main = 'upstream/' + main_branch
+
+    remote = git_repo.remotes.origin
+    remote.update(prune=True)
+    merged_branches = git_repo.git().branch(remotes=True, merged=upstream_main).split()
+    for remote_branch in merged_branches:
+        if not remote_branch or '/' not in remote_branch:
+            continue
+        if remote_branch.split('/')[1] not in (main_branch, 'HEAD'):
+            for ref in git_repo.remotes.origin.refs:
+                if remote_branch == ref.name:
+                    remote.push(':%s' % ref.remote_head, force=True)  # rm remote branch
+
+
 def status_update_json(processed: list, failed: dict) -> None:
     """Output a JSON file with metadata about this run."""
     logging.debug(_('Outputting JSON'))
diff --git a/tests/checkupdates.TestCase b/tests/checkupdates.TestCase
index 5451433a..402e3bb8 100755
--- a/tests/checkupdates.TestCase
+++ b/tests/checkupdates.TestCase
@@ -327,7 +327,7 @@ class CheckupdatesTest(unittest.TestCase):
         self.assertEqual(vername, '2')
         self.assertEqual(vercode, 2)
 
-    def test_push_commits(self):
+    def _get_test_git_repos(self):
         testdir = self.testdir.name
         os.chdir(testdir)
         os.mkdir('metadata')
@@ -338,22 +338,28 @@ class CheckupdatesTest(unittest.TestCase):
         git_repo.index.commit("all metadata files")
 
         git_remote_upstream = os.path.join(testdir, 'git_remote_upstream')
-        upstream = git.Repo.init(git_remote_upstream, bare=True)
+        upstream_repo = git.Repo.init(git_remote_upstream, bare=True)
         git_repo.create_remote('upstream', 'file://' + git_remote_upstream)
         git_remote_origin = os.path.join(testdir, 'git_remote_origin')
-        origin = git.Repo.init(git_remote_origin, bare=True)
+        origin_repo = git.Repo.init(git_remote_origin, bare=True)
         git_repo.create_remote('origin', 'file://' + git_remote_origin)
+
+        return git_repo, origin_repo, upstream_repo
+
+    def test_push_commits(self):
+        git_repo, origin_repo, upstream_repo = self._get_test_git_repos()
         for remote in git_repo.remotes:
             remote.push(git_repo.active_branch)
-        self.assertEqual(git_repo.head, upstream.head)
-        self.assertEqual(origin.head, upstream.head)
+        self.assertEqual(git_repo.head, upstream_repo.head)
+        self.assertEqual(origin_repo.head, upstream_repo.head)
         # pretend that checkupdates ran but didn't create any new commits
         fdroidserver.checkupdates.push_commits()
 
         appid = 'org.adaway'
         self.assertNotIn(appid, git_repo.branches)
+        self.assertNotIn(appid, origin_repo.branches)
+        self.assertNotIn(appid, upstream_repo.branches)
         self.assertNotIn('checkupdates', git_repo.branches)
-        self.assertNotIn(appid, git_repo.remotes.origin.repo.branches)  # TODO fix
 
         # now make commit
         app = fdroidserver.metadata.read_metadata({appid: -1})[appid]
@@ -373,6 +379,25 @@ class CheckupdatesTest(unittest.TestCase):
         self.assertNotIn('checkupdates', git_repo.branches)
         self.assertNotIn(appid, git_repo.remotes.upstream.refs)
 
+    def test_prune_empty_appid_branches(self):
+        git_repo, origin_repo, upstream_repo = self._get_test_git_repos()
+        for remote in git_repo.remotes:
+            remote.push(git_repo.active_branch)
+        self.assertEqual(git_repo.head, upstream_repo.head)
+        self.assertEqual(origin_repo.head, upstream_repo.head)
+
+        appid = 'org.adaway'
+        git_repo.create_head(appid, force=True)
+        git_repo.remotes.origin.push(appid, force=True)
+        self.assertIn(appid, git_repo.branches)
+        self.assertIn(appid, origin_repo.branches)
+        self.assertIn(appid, git_repo.remotes.origin.refs)
+        self.assertNotIn(appid, git_repo.remotes.upstream.refs)
+        fdroidserver.checkupdates.prune_empty_appid_branches()
+        self.assertNotIn(appid, origin_repo.branches)
+        self.assertNotIn(appid, git_repo.remotes.origin.refs)
+        self.assertNotIn(appid, git_repo.remotes.upstream.refs)
+
     def test_make_merge_request(self):
         testdir = self.testdir.name
         os.chdir(testdir)