diff --git a/fdroidserver/deploy.py b/fdroidserver/deploy.py
index c1423397..dd930315 100644
--- a/fdroidserver/deploy.py
+++ b/fdroidserver/deploy.py
@@ -25,7 +25,7 @@ import re
 import subprocess
 import time
 import urllib
-from git import Optional
+from typing import Optional
 import yaml
 from argparse import ArgumentParser, Namespace
 import logging
@@ -687,11 +687,22 @@ def update_servergitmirrors(servergitmirrors, repo_section):
             progress = None
 
         repo = git.Repo.init(git_mirror_path, initial_branch=GIT_BRANCH)
-        initial_commit_ref = repo.head.commit
+
+        # An initial commit of the git tree is required be for other operations
+        initial_branch_ref = repo.head.ref
+        repo.index.commit('Initial commit')
 
         enabled_remotes = []
         for d in servergitmirrors:
             index_only = d.get('index_only', False)
+            if index_only:
+                # Use a separate branch for the index only mode as it needs a different set of files to commit
+                repo.create_head('index_only', initial_branch_ref)
+                repo.heads.index_only.checkout()
+            else:
+                repo.create_head('full', initial_branch_ref)
+                repo.heads.full.checkout()
+
             remote_url = d['url']
             name = REMOTE_HOSTNAME_REGEX.sub(r'\1', remote_url)
             enabled_remotes.append(name)
@@ -777,8 +788,9 @@ def update_servergitmirrors(servergitmirrors, repo_section):
                     else:
                         logging.debug(remote.url + ': ' + pushinfo.summary)
 
-            # Reset the repository to the initial commit so we can choose which files to commit to the next remote
-            repo.head.reset(initial_commit_ref, index=True, working_tree=True)
+            # Switch to the initial branch
+            repo.head.reference = initial_branch_ref
+            repo.head.reset(index=True, working_tree=True)
 
         if progress:
             progressbar.done()