diff --git a/Annex/WorkTree.hs b/Annex/WorkTree.hs
index 30e7366396..ac9c49b27d 100644
--- a/Annex/WorkTree.hs
+++ b/Annex/WorkTree.hs
@@ -86,15 +86,16 @@ scanAnnexedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ d
 	-- The above tries to populate pointer files, but one thing it
 	-- is not able to handle is populating a pointer file when the
 	-- annex object file already exists, but its inode is not yet
-	-- cached. So, the rest of this makes another pass over the
-	-- tree to do that.
-	g <- Annex.gitRepo
-	(l, cleanup) <- inRepo $ Git.LsTree.lsTree
-		Git.LsTree.LsTreeRecursive
-		(Git.LsTree.LsTreeLong True)
-		Git.Ref.headRef
-	catObjectStreamLsTree l want g go
-	liftIO $ void cleanup
+	-- cached and annex.thin is set. So, the rest of this makes
+	-- another pass over the tree to do that.
+	whenM (annexThin <$> Annex.getGitConfig) $ do
+		g <- Annex.gitRepo
+		(l, cleanup) <- inRepo $ Git.LsTree.lsTree
+			Git.LsTree.LsTreeRecursive
+			(Git.LsTree.LsTreeLong True)
+			Git.Ref.headRef
+		catObjectStreamLsTree l want g go
+		liftIO $ void cleanup
   where
 	-- Want to process symlinks, and regular files.
 	want i = case Git.Types.toTreeItemType (Git.LsTree.mode i) of
diff --git a/Database/Keys.hs b/Database/Keys.hs
index ac8aa7f5bd..aca13f94e2 100644
--- a/Database/Keys.hs
+++ b/Database/Keys.hs
@@ -362,17 +362,25 @@ reconcileStaged qh = do
 	procmergeconflictdiff _ _ conflicted = return conflicted
 
 	reconcilepointerfile file key = do
-		caches <- liftIO $ SQL.getInodeCaches key (SQL.ReadHandle qh)
-		keyloc <- calcRepo (gitAnnexLocation key)
-		keypopulated <- sameInodeCache keyloc caches
+		ics <- liftIO $ SQL.getInodeCaches key (SQL.ReadHandle qh)
+		obj <- calcRepo (gitAnnexLocation key)
+		objic <- withTSDelta (liftIO . genInodeCache obj)
+		-- Like inAnnex, check the annex object's inode cache
+		-- when annex.thin is set.
+		keypopulated <- ifM (annexThin <$> Annex.getGitConfig)
+			( maybe (pure False) (`elemInodeCaches` ics) objic
+			, pure (isJust objic)
+			)
 		p <- fromRepo $ fromTopFilePath file
-		filepopulated <- sameInodeCache p caches
+		filepopulated <- sameInodeCache p ics
 		case (keypopulated, filepopulated) of
 			(True, False) ->
-				populatePointerFile (Restage True) key keyloc p >>= \case
+				populatePointerFile (Restage True) key obj p >>= \case
 					Nothing -> return ()
 					Just ic -> liftIO $
-						SQL.addInodeCaches key [ic] (SQL.WriteHandle qh)
+						SQL.addInodeCaches key
+							(catMaybes [Just ic, objic])
+							(SQL.WriteHandle qh)
 			(False, True) -> depopulatePointerFile key p
 			_ -> return ()