diff --git a/Annex.hs b/Annex.hs
index 84b2bda0ad..aba23587fb 100644
--- a/Annex.hs
+++ b/Annex.hs
@@ -12,6 +12,7 @@ module Annex (
 	AnnexState(..),
 	AnnexRead(..),
 	new,
+	new',
 	run,
 	eval,
 	makeRunner,
@@ -291,10 +292,13 @@ newAnnexState c r = do
  - Ensures the config is read, if it was not already, and performs
  - any necessary git repo fixups. -}
 new :: Git.Repo -> IO (AnnexState, AnnexRead)
-new r = do
+new = new' fixupRepo
+
+new' :: (Git.Repo -> GitConfig -> IO Git.Repo) -> Git.Repo -> IO (AnnexState, AnnexRead)
+new' f r = do
 	r' <- Git.Config.read r
 	let c = extractGitConfig FromGitConfig r'
-	st <- newAnnexState c =<< fixupRepo r' c
+	st <- newAnnexState c =<< f r' c
 	rd <- newAnnexRead c
 	return (st, rd)
 
diff --git a/CHANGELOG b/CHANGELOG
index d85abaa2c1..7216b21fbb 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -6,6 +6,8 @@ git-annex (10.20250631) UNRELEASED; urgency=medium
     symlinks, that caused annexed file content to be stored in the wrong
     location inside the git directory, and also caused pointer files to not
     get populated.
+  * fsck: Fix location of annexed files when run in linked worktrees
+    that have experienced the above bug.
   * Fix symlinks generated to annexed content when in adjusted unlocked
     branch in a linked worktree on a filesystem not supporting symlinks.
 
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
index 50c21149b3..cd9dd335e1 100644
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -1,6 +1,6 @@
 {- git-annex command
  -
- - Copyright 2010-2023 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2025 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -15,6 +15,7 @@ import qualified Annex
 import qualified Remote
 import qualified Types.Backend
 import qualified Backend
+import qualified Git
 import Annex.Content
 import Annex.Verify
 #ifndef mingw32_HOST_OS
@@ -24,6 +25,7 @@ import Annex.Content.Presence
 import Annex.Content.Presence.LowLevel
 import Annex.Perms
 import Annex.Link
+import Annex.Fixup
 import Logs.Location
 import Logs.Trust
 import Logs.Activity
@@ -102,6 +104,8 @@ seek o = startConcurrency commandStages $ do
 	from <- maybe (pure Nothing) (Just <$$> getParsed) (fsckFromOption o)
 	u <- maybe getUUID (pure . Remote.uuid) from
 	checkDeadRepo u
+	when (isNothing from) $
+		cleanupLinkedWorkTreeBug
 	i <- prepIncremental u (incrementalOpt o)
 	let seeker = AnnexedFileSeeker
 		{ startAction = const $ start from i
@@ -768,4 +772,38 @@ withFsckDb (ContIncremental h) a = a h
 withFsckDb (StartIncremental h) a = a h
 withFsckDb (NonIncremental mh) a = maybe noop a mh
 withFsckDb (ScheduleIncremental _ _ i) a = withFsckDb i a
-
+ 
+-- A bug caused linked worktrees on filesystems not supporting symlinks
+-- to not use the common annex directory, but one annex directory per
+-- linked worktree. Object files could end up stored in those directories.
+--
+-- When run in a linked worktree with its own annex directory that is not a
+-- symlink, move any object files to the right location, and delete the
+-- annex directory.
+cleanupLinkedWorkTreeBug :: Annex ()
+cleanupLinkedWorkTreeBug = 
+	whenM (Annex.inRepo needsGitLinkFixup) $ do
+		r <- Annex.gitRepo
+		-- mainWorkTreePath is set by fixupUnusualRepos.
+		-- Unsetting it makes a version of the Repo that uses
+		-- the wrong object location.
+		let r' = r { Git.mainWorkTreePath = Nothing }
+		let dir = gitAnnexDir r'
+		whenM (liftIO $ dirnotsymlink dir) $ do
+			showSideAction $ "Cleaning up directory " 
+				<> QuotedPath dir
+				<> " created by buggy version of git-annex"
+			(st, rd) <- liftIO $ Annex.new' (\r'' _c -> pure r'') r'
+			ks <- liftIO $ Annex.eval (st, rd) $
+				listKeys InAnnex
+			forM_ ks $ \k -> void $ tryNonAsync $ do
+				loc <- liftIO $ gitAnnexLocation k r'
+					(Annex.gitconfig st)
+				moveAnnex k loc
+			void $ tryNonAsync $ liftIO $
+				removeDirectoryRecursive dir
+  where
+	dirnotsymlink dir = 
+		tryIO (R.getSymbolicLinkStatus (fromOsPath dir)) >>= \case
+			Right st -> return $ not (isSymbolicLink st)
+			Left _ -> return False
diff --git a/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__.mdwn b/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__.mdwn
index bbbb8143b3..9aa0d48d6d 100644
--- a/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__.mdwn
+++ b/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__.mdwn
@@ -97,3 +97,5 @@ This is on win11.
 Absolutely! Approaching 15 years of bigger, better, faster, more ;-)
 
 [[!tag projects/INM7]]
+
+> [[fixed|done]] --[[Joey]]
diff --git a/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__/comment_7_cfb97162cd21818995f9d71a5ce3a0d0._comment b/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__/comment_7_cfb97162cd21818995f9d71a5ce3a0d0._comment
new file mode 100644
index 0000000000..bb752665bf
--- /dev/null
+++ b/doc/bugs/Missing_file_content_in_secondary_worktree___40__win__41__/comment_7_cfb97162cd21818995f9d71a5ce3a0d0._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 7"""
+ date="2025-07-15T17:07:43Z"
+ content="""
+Running `git-annex fsck` in the affected worktree will clean up from this
+bug.
+"""]]