diff --git a/mercurial/exchange.py b/mercurial/exchange.py
--- a/mercurial/exchange.py
+++ b/mercurial/exchange.py
@@ -1658,6 +1658,10 @@ def _maybeapplyclonebundle(pullop):
     if not repo.ui.configbool('experimental', 'clonebundles', False):
         return
 
+    # Only run if local repo is empty.
+    if len(repo):
+        return
+
     if pullop.heads:
         return
 
diff --git a/tests/test-clonebundles.t b/tests/test-clonebundles.t
--- a/tests/test-clonebundles.t
+++ b/tests/test-clonebundles.t
@@ -167,12 +167,6 @@ Incremental pull doesn't fetch bundle
   $ cd partial-clone
   $ hg pull
   pulling from http://localhost:$HGPORT/
-  applying clone bundle from http://localhost:$HGPORT1/partial.hg
-  adding changesets
-  adding manifests
-  adding file changes
-  added 0 changesets with 0 changes to 1 files
-  finished applying clone bundle
   searching for changes
   adding changesets
   adding manifests