diff --git a/fdroidserver/deploy.py b/fdroidserver/deploy.py
index 68a40906..a17d7468 100644
--- a/fdroidserver/deploy.py
+++ b/fdroidserver/deploy.py
@@ -793,6 +793,7 @@ def update_servergitmirrors(servergitmirrors, repo_section):
             # Switch to the initial branch and unstage all files
             repo.head.reference = initial_branch_ref
             repo.head.reset(index=True, working_tree=False)
+            repo.delete_head(repo.branches[branch_name])
 
         if progress:
             progressbar.done()