diff --git a/fdroidserver/deploy.py b/fdroidserver/deploy.py
index c624e874..e0c61363 100644
--- a/fdroidserver/deploy.py
+++ b/fdroidserver/deploy.py
@@ -797,9 +797,11 @@ def upload_to_servergitmirror(
     logging.info('Mirroring to: ' + remote_url)
 
     if is_index_only:
-        local_repo.index.add(
-            _get_index_file_paths(os.path.join('fdroid', repo_section))
+        files_to_upload = _get_index_file_paths(
+            os.path.join(local_repo.working_tree_dir, 'fdroid', repo_section)
         )
+        files_to_upload = _remove_missing_files(files_to_upload)
+        local_repo.index.add(files_to_upload)
     else:
         # sadly index.add don't allow the --all parameter
         logging.debug('Adding all files to git mirror')