diff --git a/Annex/Branch.hs b/Annex/Branch.hs
index 8192804a6b..bc6c8fe542 100644
--- a/Annex/Branch.hs
+++ b/Annex/Branch.hs
@@ -29,6 +29,7 @@ module Annex.Branch (
 import qualified Data.ByteString.Lazy.Char8 as L
 import qualified Data.Set as S
 import qualified Data.Map as M
+import qualified Control.Exception as E
 
 import Common.Annex
 import Annex.BranchState
@@ -53,6 +54,7 @@ import Logs.Trust.Pure
 import Annex.ReplaceFile
 import qualified Annex.Queue
 import Annex.Branch.Transitions
+import Annex.Exception
 
 {- Name of the branch that is used to store git-annex's information. -}
 name :: Git.Ref
@@ -345,15 +347,15 @@ withIndex' bootstrapping a = do
 #endif
 	let g' = g { gitEnv = Just $ ("GIT_INDEX_FILE", f):e }
 
-	Annex.changeState $ \s -> s { Annex.repo = g' }
-	checkIndexOnce $ unlessM (liftIO $ doesFileExist f) $ do
-		unless bootstrapping create
-		liftIO $ createDirectoryIfMissing True $ takeDirectory f
-		unless bootstrapping $ inRepo genIndex
-	r <- a
+	r <- tryAnnex $ do
+		Annex.changeState $ \s -> s { Annex.repo = g' }
+		checkIndexOnce $ unlessM (liftIO $ doesFileExist f) $ do
+			unless bootstrapping create
+			liftIO $ createDirectoryIfMissing True $ takeDirectory f
+			unless bootstrapping $ inRepo genIndex
+		a
 	Annex.changeState $ \s -> s { Annex.repo = (Annex.repo s) { gitEnv = gitEnv g} }
-
-	return r
+	either Ethrow return r
 
 {- Updates the branch's index to reflect the current contents of the branch.
  - Any changes staged in the index will be preserved.
diff --git a/debian/changelog b/debian/changelog
index 94c68b42c4..17911cab53 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -13,6 +13,9 @@ git-annex (4.20131106) unstable; urgency=low
     views in the webapp.
   * map: Work when there are gcrypt remotes.
   * Fix build w/o webapp.
+  * Fix exception handling bug that could cause .git/annex/index to be used
+    for git commits outside the git-annex branch. Known to affect git-annex
+    when used with the git shipped with Ubuntu 13.10.
 
  -- Joey Hess <joeyh@debian.org>  Wed, 06 Nov 2013 11:17:47 -0400
 
diff --git a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn
index ca8e765bc0..d66196acd3 100644
--- a/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn
+++ b/doc/bugs/Freshly_initialized_repo_has_staged_change___34__deleted:_uuid.log__34__.mdwn
@@ -40,3 +40,5 @@ Perhaps some sort of a race-condition with the annex-assistant picking up the uu
 
 ### What version of git-annex are you using? On what operating system?
 Ubuntu 13.10 with git-annex 4.20130815
+
+> [[fixed|done]]; see comments. (This fix needs to be backported to Ubuntu.) --[[Joey]]