diff --git a/Assistant/WebApp/Configurators/Preferences.hs b/Assistant/WebApp/Configurators/Preferences.hs
index 2bd161351d..75df8ebf17 100644
--- a/Assistant/WebApp/Configurators/Preferences.hs
+++ b/Assistant/WebApp/Configurators/Preferences.hs
@@ -18,9 +18,9 @@ import qualified Git
 import Config
 import Config.Files
 import Utility.DataUnits
+import Git.Config
 
 import qualified Data.Text as T
-import System.Log.Logger
 
 data PrefsForm = PrefsForm
 	{ diskReserve :: Text
@@ -68,7 +68,7 @@ getPrefs = PrefsForm
 	<$> (T.pack . roughSize storageUnits False . annexDiskReserve <$> Annex.getGitConfig)
 	<*> (annexNumCopies <$> Annex.getGitConfig)
 	<*> inAutoStartFile
-	<*> ((==) <$> (pure $ Just DEBUG) <*> (liftIO $ getLevel <$> getRootLogger))
+	<*> (annexDebug <$> Annex.getGitConfig)
 
 storePrefs :: PrefsForm -> Annex ()
 storePrefs p = do
@@ -79,8 +79,10 @@ storePrefs p = do
 		liftIO $ if autoStart p
 			then addAutoStartFile here
 			else removeAutoStartFile here
-	liftIO $ updateGlobalLogger rootLoggerName $ setLevel $
-		if debugEnabled p then DEBUG else WARNING
+	setConfig (annexConfig "debug") (boolConfig $ debugEnabled p)
+	liftIO $ if debugEnabled p
+		then enableDebugOutput 
+		else disableDebugOutput
 
 getPreferencesR :: Handler RepHtml
 getPreferencesR = postPreferencesR
diff --git a/CmdLine.hs b/CmdLine.hs
index 8f4c992699..d9a4103696 100644
--- a/CmdLine.hs
+++ b/CmdLine.hs
@@ -48,6 +48,8 @@ dispatch fuzzyok allargs allcmds commonoptions fields header getgitrepo = do
 				checkfuzzy
 				forM_ fields $ uncurry Annex.setField
 				sequence_ flags
+				whenM (annexDebug <$> Annex.getGitConfig) $
+					liftIO enableDebugOutput
 				prepCommand cmd params
 		 	tryRun state' cmd $ [startup] ++ actions ++ [shutdown $ cmdnocommit cmd]
   where
diff --git a/Messages.hs b/Messages.hs
index b2fcba881b..0357da12df 100644
--- a/Messages.hs
+++ b/Messages.hs
@@ -31,7 +31,9 @@ module Messages (
 	showCustom,
 	showHeader,
 	showRaw,
-	setupConsole
+	setupConsole,
+	enableDebugOutput,
+	disableDebugOutput
 ) where
 
 import Text.JSON
@@ -220,6 +222,12 @@ setupConsole = do
 	fileEncoding stdout
 	fileEncoding stderr
 
+enableDebugOutput :: IO ()
+enableDebugOutput = updateGlobalLogger rootLoggerName $ setLevel DEBUG
+
+disableDebugOutput :: IO ()
+disableDebugOutput = updateGlobalLogger rootLoggerName $ setLevel NOTICE
+
 handle :: IO () -> IO () -> Annex ()
 handle json normal = withOutputType go
   where
diff --git a/Option.hs b/Option.hs
index d59af43c7a..64ba56f6d2 100644
--- a/Option.hs
+++ b/Option.hs
@@ -16,7 +16,6 @@ module Option (
 ) where
 
 import System.Console.GetOpt
-import System.Log.Logger
 
 import Common.Annex
 import qualified Annex
@@ -40,6 +39,8 @@ common =
 		"enable JSON output"
 	, Option ['d'] ["debug"] (NoArg setdebug)
 		"show debug messages"
+	, Option [] ["no-debug"] (NoArg unsetdebug)
+		"don't show debug messages"
 	, Option ['b'] ["backend"] (ReqArg setforcebackend paramName)
 		"specify key-value backend to use"
 	]
@@ -48,7 +49,8 @@ common =
 	setfast v = Annex.changeState $ \s -> s { Annex.fast = v }
 	setauto v = Annex.changeState $ \s -> s { Annex.auto = v }
 	setforcebackend v = Annex.changeState $ \s -> s { Annex.forcebackend = Just v }
-	setdebug = liftIO $ updateGlobalLogger rootLoggerName $ setLevel DEBUG
+	setdebug = Annex.changeGitConfig $ \c -> c { annexDebug = True }
+	unsetdebug = Annex.changeGitConfig $ \c -> c { annexDebug = False }
 
 matcher :: [Option]
 matcher =
diff --git a/Types/GitConfig.hs b/Types/GitConfig.hs
index 888795cbbc..d5d234ca93 100644
--- a/Types/GitConfig.hs
+++ b/Types/GitConfig.hs
@@ -35,6 +35,7 @@ data GitConfig = GitConfig
 	, annexHttpHeaders :: [String]
 	, annexHttpHeadersCommand :: Maybe String
 	, annexAutoCommit :: Bool
+	, annexDebug :: Bool
 	, annexWebOptions :: [String]
 	, annexWebDownloadCommand :: Maybe String
 	, annexCrippledFileSystem :: Bool
@@ -59,6 +60,7 @@ extractGitConfig r = GitConfig
 	, annexHttpHeaders = getlist (annex "http-headers")
 	, annexHttpHeadersCommand = getmaybe (annex "http-headers-command")
 	, annexAutoCommit = getbool (annex "autocommit") True
+	, annexDebug = getbool (annex "debug") False
 	, annexWebOptions = getwords (annex "web-options")
 	, annexWebDownloadCommand = getmaybe (annex "web-download-command")
 	, annexCrippledFileSystem = getbool (annex "crippledfilesystem") False
diff --git a/debian/changelog b/debian/changelog
index e51c769c30..c433d2bf04 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -28,6 +28,8 @@ git-annex (4.20130602) UNRELEASED; urgency=low
     area, since it does not keep track of associated files.)
     Closes: #712060
   * status: No longer shows dead repositories.
+  * annex.debug can now be set to enable debug logging by default.
+    The webapp's debugging check box does this.
 
  -- Joey Hess <joeyh@debian.org>  Mon, 10 Jun 2013 12:52:44 -0400
 
diff --git a/doc/git-annex.mdwn b/doc/git-annex.mdwn
index 18bc05ad27..f0da25e146 100644
--- a/doc/git-annex.mdwn
+++ b/doc/git-annex.mdwn
@@ -622,6 +622,10 @@ subdirectories).
 
   Show debug messages.
 
+* --no-debug
+
+  Disable debug messages.
+
 * --from=repository
 
   Specifies a repository that content will be retrieved from, or that
@@ -903,6 +907,10 @@ Here are all the supported configuration settings.
   Set to false to prevent the git-annex assistant from automatically
   committing changes to files in the repository.
 
+* `annex.debug`
+
+  Set to true to enable debug logging by default.
+
 * `annex.version`
 
   Automatically maintained, and used to automate upgrades between versions.