diff --git a/Annex/Init.hs b/Annex/Init.hs
index 8c03dda835..5b34af4238 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -37,6 +37,7 @@ import Annex.UUID
 import Annex.WorkTree
 import Annex.Fixup
 import Annex.Path
+import Annex.GitOverlay
 import Config
 import Config.Files
 import Config.Smudge
@@ -326,7 +327,7 @@ fixupUnusualReposAfterInit = do
  - The enabling is done in a child process to avoid it using stdio.
  -}
 autoEnableSpecialRemotes :: Annex ()
-autoEnableSpecialRemotes = do
+autoEnableSpecialRemotes = runsGitAnnexChildProcess $ do
 	rp <- fromRawFilePath <$> fromRepo Git.repoPath
 	cmd <- liftIO programPath
 	liftIO $ withNullHandle $ \nullh -> do
diff --git a/Command/Sync.hs b/Command/Sync.hs
index 5bd65b2df3..f8a6852a38 100644
--- a/Command/Sync.hs
+++ b/Command/Sync.hs
@@ -65,6 +65,7 @@ import Annex.UpdateInstead
 import Annex.Export
 import Annex.TaggedPush
 import Annex.CurrentBranch
+import Annex.GitOverlay
 import qualified Database.Export as Export
 import Utility.Bloom
 import Utility.OptParse
@@ -513,7 +514,7 @@ pushRemote o remote (Just branch, _) = do
 	postpushupdate repo = case Git.repoWorkTree repo of
 		Nothing -> return True
 		Just wt -> ifM needemulation
-			( liftIO $ do
+			( runsGitAnnexChildProcess $ liftIO $ do
 				p <- programPath
 				boolSystem' p [Param "post-receive"]
 					(\cp -> cp { cwd = Just (fromRawFilePath wt) })
diff --git a/Upgrade.hs b/Upgrade.hs
index 6879fd7bea..76aac93afe 100644
--- a/Upgrade.hs
+++ b/Upgrade.hs
@@ -15,6 +15,7 @@ import qualified Git
 import Config
 import Annex.Path
 import Annex.Version
+import Annex.GitOverlay
 import Types.RepoVersion
 #ifndef mingw32_HOST_OS
 import qualified Upgrade.V0
@@ -104,7 +105,7 @@ upgrade automatic destversion = do
 	upgraderemote = do
 		rp <- fromRawFilePath <$> fromRepo Git.repoPath
 		cmd <- liftIO programPath
-		liftIO $ boolSystem' cmd
+		runsGitAnnexChildProcess $ liftIO $ boolSystem' cmd
 			[ Param "upgrade"
 			, Param "--quiet"
 			, Param "--autoonly"