diff --git a/fdroidserver/deploy.py b/fdroidserver/deploy.py
index b56c5c40..68a40906 100644
--- a/fdroidserver/deploy.py
+++ b/fdroidserver/deploy.py
@@ -790,9 +790,9 @@ def update_servergitmirrors(servergitmirrors, repo_section):
                     else:
                         logging.debug(remote.url + ': ' + pushinfo.summary)
 
-            # Switch to the initial branch
+            # Switch to the initial branch and unstage all files
             repo.head.reference = initial_branch_ref
-            repo.head.reset(index=True, working_tree=True)
+            repo.head.reset(index=True, working_tree=False)
 
         if progress:
             progressbar.done()