diff --git a/Annex/GitOverlay.hs b/Annex/GitOverlay.hs
index 2193b74498..1b7ceb2e2d 100644
--- a/Annex/GitOverlay.hs
+++ b/Annex/GitOverlay.hs
@@ -15,6 +15,7 @@ import Git.Types
 import Git.Index
 import Git.Env
 import qualified Annex
+import qualified Annex.Queue
 
 {- Runs an action using a different git index file. -}
 withIndexFile :: FilePath -> Annex a -> Annex a
@@ -71,8 +72,18 @@ withAltRepo
 withAltRepo modrepo unmodrepo a = do
 	g <- gitRepo
 	g' <- liftIO $ modrepo g
-	r <- tryNonAsync $ do
-		Annex.changeState $ \s -> s { Annex.repo = g' }
+	q <- Annex.Queue.get
+	v <- tryNonAsync $ do
+		Annex.changeState $ \s -> s
+			{ Annex.repo = g'
+			-- Start a separate queue for any changes made
+			-- with the modified repo.
+			, Annex.repoqueue = Nothing
+			}
 		a
-	Annex.changeState $ \s -> s { Annex.repo = unmodrepo g (Annex.repo s) }
-	either E.throw return r
+	void $ tryNonAsync Annex.Queue.flush
+	Annex.changeState $ \s -> s
+		{ Annex.repo = unmodrepo g (Annex.repo s)
+		, Annex.repoqueue = Just q
+		}
+	either E.throw return v
diff --git a/Annex/Queue.hs b/Annex/Queue.hs
index 0e1b0f68cc..9c22e75fd0 100644
--- a/Annex/Queue.hs
+++ b/Annex/Queue.hs
@@ -13,6 +13,7 @@ module Annex.Queue (
 	flush,
 	flushWhenFull,
 	size,
+	get,
 	mergeFrom,
 ) where