diff --git a/bitbake/lib/bb/fetch2/git.py b/bitbake/lib/bb/fetch2/git.py
index 2a3c06fe4e9..112bed294f0 100644
--- a/bitbake/lib/bb/fetch2/git.py
+++ b/bitbake/lib/bb/fetch2/git.py
@@ -65,6 +65,7 @@ import fnmatch
 import os
 import re
 import shlex
+import shutil
 import subprocess
 import tempfile
 import bb
@@ -365,8 +366,29 @@ class Git(FetchMethod):
                 runfetchcmd(fetch_cmd, d, workdir=ud.clonedir)
         repourl = self._get_repo_url(ud)
 
+        needs_clone = False
+        if os.path.exists(ud.clonedir):
+            # The directory may exist, but not be the top level of a bare git
+            # repository in which case it needs to be deleted and re-cloned.
+            try:
+                # Since clones are bare, use --absolute-git-dir instead of --show-toplevel
+                output = runfetchcmd("LANG=C %s rev-parse --absolute-git-dir" % ud.basecmd, d, workdir=ud.clonedir)
+            except bb.fetch2.FetchError as e:
+                logger.warning("Unable to get top level for %s (not a git directory?): %s", ud.clonedir, e)
+                needs_clone = True
+            else:
+                toplevel = output.rstrip()
+                if os.path.abspath(toplevel) != os.path.abspath(ud.clonedir):
+                    logger.warning("Top level directory '%s' doesn't match expected '%s'. Re-cloning", toplevel, ud.clonedir)
+                    needs_clone = True
+
+            if needs_clone:
+                shutil.rmtree(ud.clonedir)
+        else:
+            needs_clone = True
+
         # If the repo still doesn't exist, fallback to cloning it
-        if not os.path.exists(ud.clonedir):
+        if needs_clone:
             # We do this since git will use a "-l" option automatically for local urls where possible,
             # but it doesn't work when git/objects is a symlink, only works when it is a directory.
             if repourl.startswith("file://"):