diff --git a/CHANGELOG b/CHANGELOG
index 254f914b59..7e523186c6 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -15,6 +15,8 @@ git-annex (10.20241032) UNRELEASED; urgency=medium
     unversioned S3 bucket that is large enough to need pagination.
   * S3: Use significantly less memory when importing from a
     versioned S3 bucket.
+  * git-remote-annex: Fix cloning from a special remote on a crippled
+    filesystem.
 
  -- Joey Hess <id@joeyh.name>  Mon, 11 Nov 2024 12:26:00 -0400
 
diff --git a/CmdLine/GitRemoteAnnex.hs b/CmdLine/GitRemoteAnnex.hs
index 36d2446e4e..89ded7191c 100644
--- a/CmdLine/GitRemoteAnnex.hs
+++ b/CmdLine/GitRemoteAnnex.hs
@@ -1129,7 +1129,7 @@ specialRemoteFromUrl sab a = withTmpDir "journal" $ \tmpdir -> do
 -- If the git-annex branch did not exist when this command started,
 -- it was created empty by this command, and this command has avoided
 -- making any other commits to it, writing any temporary annex branch
--- changes to thre alternateJournal, which can now be discarded. 
+-- changes to the alternateJournal, which can now be discarded. 
 -- 
 -- If nothing else has written to the branch while this command was running,
 -- the branch will be deleted. That allows for the git-annex branch that is
@@ -1152,6 +1152,11 @@ specialRemoteFromUrl sab a = withTmpDir "journal" $ \tmpdir -> do
 -- does not contain any hooks. Since initialization installs
 -- hooks, have to work around that by not initializing, and 
 -- delete the git bundle objects.
+--
+-- Similarly, when on a crippled filesystem, doing initialization would
+-- involve checking out an adjusted branch. But git clone wants to do its
+-- own checkout. So no initialization is done then, and the git bundle
+-- objects are deleted.
 cleanupInitialization :: StartAnnexBranch -> FilePath -> Annex ()
 cleanupInitialization sab alternatejournaldir = void $ tryNonAsync $ do
 	liftIO $ mapM_ removeFile =<< dirContents alternatejournaldir
@@ -1173,7 +1178,7 @@ cleanupInitialization sab alternatejournaldir = void $ tryNonAsync $ do
 					Nothing -> return ()
 					Just _ -> void $ tryNonAsync $
 						inRepo $ Git.Branch.delete Annex.Branch.fullname
-	ifM (Annex.Branch.hasSibling <&&> nonbuggygitversion)
+	ifM (Annex.Branch.hasSibling <&&> nonbuggygitversion <&&> notcrippledfilesystem)
 		( do
 			autoInitialize' (pure True) startupAnnex remoteList
 			differences <- allDifferences <$> recordedDifferences
@@ -1190,6 +1195,8 @@ cleanupInitialization sab alternatejournaldir = void $ tryNonAsync $ do
 			_ -> noop
 		void $ liftIO $ tryIO $ removeDirectory (decodeBS annexobjectdir)
 
+	notcrippledfilesystem = not <$> probeCrippledFileSystem
+
 	nonbuggygitversion = liftIO $
 		flip notElem buggygitversions <$> Git.Version.installed
 	buggygitversions = map Git.Version.normalize
diff --git a/doc/bugs/tests_started_to_fail_recently/comment_1_c07a23f5d8524ba8f97187ade6eeb441._comment b/doc/bugs/tests_started_to_fail_recently/comment_1_c07a23f5d8524ba8f97187ade6eeb441._comment
new file mode 100644
index 0000000000..8f4197908f
--- /dev/null
+++ b/doc/bugs/tests_started_to_fail_recently/comment_1_c07a23f5d8524ba8f97187ade6eeb441._comment
@@ -0,0 +1,17 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 1"""
+ date="2024-11-19T16:18:31Z"
+ content="""
+This is a new test.
+
+Looks like it's found a legitimate bug in git-remote-annex. When the
+filesystem is crippled, the git-annex init checks out an adjusted branch,
+which here happens in the middle of git's own checkout and so legitimately
+confuses git.
+
+I can reproduce this on a FAT filesystem, cloning from eg a directory
+special remote. Fixed this.
+
+(The OSX failure is something else.)
+"""]]