diff --git a/Annex/Init.hs b/Annex/Init.hs
index 1bc82710f4..a762bf690c 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -108,9 +108,9 @@ initialize' mversion = checkCanInitialize  $ do
 	unlessM (isJust <$> getVersion) $
 		setVersion (fromMaybe defaultVersion mversion)
 	configureSmudgeFilter
-	showSideAction "scanning for unlocked files"
-	scanUnlockedFiles
 	unlessM isBareRepo $ do
+		showSideAction "scanning for unlocked files"
+		scanUnlockedFiles
 		hookWrite postCheckoutHook
 		hookWrite postMergeHook
 	AdjustedBranch.checkAdjustedClone >>= \case
diff --git a/Annex/WorkTree.hs b/Annex/WorkTree.hs
index cf40f527bf..b04eeac4d8 100644
--- a/Annex/WorkTree.hs
+++ b/Annex/WorkTree.hs
@@ -22,6 +22,7 @@ import qualified Git.Types
 import Database.Types
 import qualified Database.Keys
 import qualified Database.Keys.SQL
+import Config
 
 {- Looks up the key corresponding to an annexed file in the work tree,
  - by examining what the file links to.
@@ -75,7 +76,7 @@ ifAnnexed file yes no = maybe no yes =<< lookupFile file
  - as-is.
  -}
 scanUnlockedFiles :: Annex ()
-scanUnlockedFiles = whenM (inRepo Git.Ref.headExists) $ do
+scanUnlockedFiles = whenM (inRepo Git.Ref.headExists <&&> not <$> isBareRepo) $ do
 	Database.Keys.runWriter $
 		liftIO . Database.Keys.SQL.dropAllAssociatedFiles
 	(l, cleanup) <- inRepo $ Git.LsTree.lsTree Git.LsTree.LsTreeRecursive Git.Ref.headRef