diff --git a/Annex/Init.hs b/Annex/Init.hs
index 5acfccf7f6..d7c1ebd9ed 100644
--- a/Annex/Init.hs
+++ b/Annex/Init.hs
@@ -1,6 +1,6 @@
 {- git-annex repository initialization
  -
- - Copyright 2011-2019 Joey Hess <id@joeyh.name>
+ - Copyright 2011-2020 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -35,11 +35,13 @@ import Annex.Difference
 import Annex.UUID
 import Annex.WorkTree
 import Annex.Fixup
+import Annex.Path
 import Config
 import Config.Files
 import Config.Smudge
 import qualified Upgrade.V5.Direct as Direct
 import qualified Annex.AdjustedBranch as AdjustedBranch
+import Remote.List.Util (remotesChanged)
 import Annex.Environment
 import Annex.Hook
 import Annex.InodeSentinal
@@ -150,8 +152,10 @@ ensureInitialized :: Annex ()
 ensureInitialized = getVersion >>= maybe needsinit checkUpgrade
   where
 	needsinit = ifM Annex.Branch.hasSibling
-		( initialize Nothing Nothing
-		, giveup $ "First run: git-annex init"
+		( do
+			initialize Nothing Nothing
+			autoEnableSpecialRemotes
+		, giveup "First run: git-annex init"
 		)
 
 {- Checks if a repository is initialized. Does not check version for ugrade. -}
@@ -287,3 +291,25 @@ fixupUnusualReposAfterInit :: Annex ()
 fixupUnusualReposAfterInit = do
 	gc <- Annex.getGitConfig
 	void $ inRepo $ \r -> fixupUnusualRepos r gc
+
+{- Try to enable any special remotes that are configured to do so.
+ - 
+ - The enabling is done in a child process to avoid it using stdio.
+ -}
+autoEnableSpecialRemotes :: Annex ()
+autoEnableSpecialRemotes = do
+	rp <- fromRawFilePath <$> fromRepo Git.repoPath
+	cmd <- liftIO programPath
+	liftIO $ withNullHandle $ \nullh -> do
+		let p = proc cmd 
+			[ "init"
+			, "--autoenable"
+			]
+		(Nothing, Nothing, Nothing, pid) <- createProcess $ p
+			{ std_out = UseHandle nullh
+			, std_err = UseHandle nullh
+			, std_in = UseHandle nullh
+			, cwd = Just rp
+			}
+		void $ waitForProcess pid
+	remotesChanged
diff --git a/Assistant/DeleteRemote.hs b/Assistant/DeleteRemote.hs
index c7cf807831..f0743401bd 100644
--- a/Assistant/DeleteRemote.hs
+++ b/Assistant/DeleteRemote.hs
@@ -16,7 +16,7 @@ import Types.Transfer
 import Logs.Location
 import Assistant.DaemonStatus
 import qualified Remote
-import Remote.List
+import Remote.List.Util
 import qualified Git.Remote.Remove
 import Logs.Trust
 import qualified Annex
@@ -35,7 +35,7 @@ disableRemote uuid = do
 		<$> liftAnnex (Remote.remoteFromUUID uuid)
 	liftAnnex $ do
 		inRepo $ Git.Remote.Remove.remove (Remote.name remote)
-		void $ remoteListRefresh
+		remotesChanged
 	updateSyncRemotes
 	return remote
 
diff --git a/Assistant/MakeRemote.hs b/Assistant/MakeRemote.hs
index 3b36ef9a51..45ceb01337 100644
--- a/Assistant/MakeRemote.hs
+++ b/Assistant/MakeRemote.hs
@@ -13,7 +13,7 @@ import Assistant.Common
 import Assistant.Ssh
 import qualified Types.Remote as R
 import qualified Remote
-import Remote.List
+import Remote.List.Util
 import qualified Remote.Rsync as Rsync
 import qualified Remote.GCrypt as GCrypt
 import qualified Git
@@ -46,7 +46,7 @@ makeSshRemote sshdata = maker (sshRepoName sshdata) (genSshUrl sshdata)
 addRemote :: Annex RemoteName -> Annex Remote
 addRemote a = do
 	name <- a
-	void remoteListRefresh
+	remotesChanged
 	maybe (error "failed to add remote") return
 		=<< Remote.byName (Just name)
 
@@ -174,7 +174,9 @@ previouslyUsedCredPair
 	-> (Remote -> Bool)
 	-> Annex (Maybe CredPair)
 previouslyUsedCredPair getstorage remotetype criteria =
-	getM fromstorage =<< filter criteria . filter sametype <$> remoteList
+	getM fromstorage
+		=<< filter criteria . filter sametype 
+		<$> Remote.remoteList
   where
 	sametype r = R.typename (R.remotetype r) == R.typename remotetype
 	fromstorage r = do
diff --git a/Assistant/Sync.hs b/Assistant/Sync.hs
index 5b19d5216a..2b0fae5c97 100644
--- a/Assistant/Sync.hs
+++ b/Assistant/Sync.hs
@@ -22,8 +22,8 @@ import qualified Git
 import qualified Git.Command
 import qualified Remote
 import qualified Types.Remote as Remote
-import qualified Remote.List as Remote
 import qualified Annex.Branch
+import Remote.List.Util
 import Annex.UUID
 import Annex.TaggedPush
 import Annex.Ssh
@@ -268,7 +268,7 @@ changeSyncFlag r enabled = do
 	repo <- Remote.getRepo r
 	let key = Config.remoteAnnexConfig repo "sync"
 	Config.setConfig key (boolConfig enabled)
-	void Remote.remoteListRefresh
+	remotesChanged
 
 updateExportTreeFromLogAll :: Assistant ()
 updateExportTreeFromLogAll = do
diff --git a/Assistant/Threads/ConfigMonitor.hs b/Assistant/Threads/ConfigMonitor.hs
index b8ccb9e23d..a0d748df66 100644
--- a/Assistant/Threads/ConfigMonitor.hs
+++ b/Assistant/Threads/ConfigMonitor.hs
@@ -18,7 +18,7 @@ import Logs.Trust
 import Logs.PreferredContent
 import Logs.Group
 import Logs.NumCopies
-import Remote.List (remoteListRefresh)
+import Remote.List.Util
 import qualified Git.LsTree as LsTree
 import Git.Types
 import Git.FilePath
@@ -60,7 +60,7 @@ type Configs = S.Set (RawFilePath, Sha)
 configFilesActions :: [(RawFilePath, Assistant ())]
 configFilesActions =
 	[ (uuidLog, void $ liftAnnex uuidDescMapLoad)
-	, (remoteLog, void $ liftAnnex remoteListRefresh)
+	, (remoteLog, void $ liftAnnex remotesChanged)
 	, (trustLog, void $ liftAnnex trustMapLoad)
 	, (groupLog, void $ liftAnnex groupMapLoad)
 	, (numcopiesLog, void $ liftAnnex globalNumCopiesLoad)
diff --git a/Assistant/WebApp/Configurators/Edit.hs b/Assistant/WebApp/Configurators/Edit.hs
index c82fbe248f..cacacdc024 100644
--- a/Assistant/WebApp/Configurators/Edit.hs
+++ b/Assistant/WebApp/Configurators/Edit.hs
@@ -25,7 +25,7 @@ import qualified Remote.S3 as S3
 #endif
 import qualified Remote
 import qualified Types.Remote as Remote
-import qualified Remote.List as Remote
+import Remote.List.Util
 import Logs.UUID
 import Logs.Group
 import Logs.PreferredContent
@@ -116,7 +116,7 @@ setRepoConfig uuid mremote oldc newc = do
 				, Param $ T.unpack $ repoName oldc
 				, Param name
 				]
-			void Remote.remoteListRefresh
+			remotesChanged
 		liftAssistant updateSyncRemotes
 	when associatedDirectoryChanged $ case repoAssociatedDirectory newc of
 		Nothing -> noop
@@ -309,7 +309,7 @@ getUpgradeRepositoryR r = go =<< liftAnnex (repoIdRemote r)
 			setConfig
 				(remoteAnnexConfig repo "ignore")
 				(Git.Config.boolConfig False)
-		liftAnnex $ void Remote.remoteListRefresh
+		liftAnnex remotesChanged
 		liftAssistant updateSyncRemotes
 		liftAssistant $ syncRemote rmt
 		redirect DashboardR
diff --git a/Assistant/WebApp/RepoList.hs b/Assistant/WebApp/RepoList.hs
index f388dd77b9..9fcca1ae26 100644
--- a/Assistant/WebApp/RepoList.hs
+++ b/Assistant/WebApp/RepoList.hs
@@ -14,7 +14,7 @@ import Assistant.DaemonStatus
 import Assistant.WebApp.Notifications
 import qualified Remote
 import qualified Types.Remote as Remote
-import Remote.List (remoteListRefresh)
+import Remote.List.Util
 import Annex.UUID (getUUID)
 import Logs.Remote
 import Logs.Trust
@@ -242,7 +242,7 @@ getRepositoriesReorderR = do
 			when (Remote.cost r /= newcost) $ do
 				repo <- Remote.getRepo r
 				setRemoteCost repo newcost
-		void remoteListRefresh
+		remotesChanged
 	fromjs = fromMaybe (RepoUUID NoUUID) . readish . T.unpack
 
 reorderCosts :: Remote -> [Remote] -> [(Remote, Cost)]
diff --git a/CHANGELOG b/CHANGELOG
index b19ab01110..95dd7fe9f8 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,5 +1,11 @@
 git-annex (8.20200523) UNRELEASED; urgency=medium
 
+  * Try to enable special remotes configured with autoenable=yes
+    when git-annex auto-initialization happens in a new clone of an
+    existing repo. Previously, git-annex init had to be explicitly run to
+    enable them. Special remotes cannot display anything when autoenabled
+    this way, to avoid interfering with the output of git-annex query
+    commands.
   * export: Added options for json output.
   * import: Added --json-progress.
   * addurl: Make --preserve-filename also apply when eg a torrent contains
diff --git a/Command/Init.hs b/Command/Init.hs
index 65bb05ca0b..b79f5be635 100644
--- a/Command/Init.hs
+++ b/Command/Init.hs
@@ -1,6 +1,6 @@
 {- git-annex command
  -
- - Copyright 2010 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2020 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -24,6 +24,7 @@ cmd = dontCheck repoExists $
 data InitOptions = InitOptions
 	{ initDesc :: String
 	, initVersion :: Maybe RepoVersion
+	, autoEnableOnly :: Bool
 	}
 
 optParser :: CmdParamsDesc -> Parser InitOptions
@@ -33,6 +34,10 @@ optParser desc = InitOptions
 		( long "version" <> metavar paramValue
 		<> help "Override default annex.version"
 		))
+	<*> switch
+		( long "autoenable"
+		<> help "only enable special remotes configured with autoenable=true"
+		)
 
 parseRepoVersion :: MonadFail m => String -> m RepoVersion
 parseRepoVersion s = case RepoVersion <$> readish s of
@@ -47,8 +52,11 @@ seek :: InitOptions -> CommandSeek
 seek = commandAction . start
 
 start :: InitOptions -> CommandStart
-start os = starting "init" (ActionItemOther (Just $ initDesc os)) $
-	perform os
+start os
+	| autoEnableOnly os = starting "init" (ActionItemOther (Just "autoenable")) $
+		performAutoEnableOnly
+	| otherwise = starting "init" (ActionItemOther (Just $ initDesc os)) $
+		perform os
 
 perform :: InitOptions -> CommandPerform
 perform os = do
@@ -63,3 +71,8 @@ perform os = do
 		(initVersion os)
 	Annex.SpecialRemote.autoEnable
 	next $ return True
+
+performAutoEnableOnly :: CommandPerform
+performAutoEnableOnly = do
+	Annex.SpecialRemote.autoEnable
+	next $ return True
diff --git a/Remote.hs b/Remote.hs
index 6670925df0..581a035eaf 100644
--- a/Remote.hs
+++ b/Remote.hs
@@ -74,6 +74,7 @@ import Logs.Trust
 import Logs.Location hiding (logStatus)
 import Logs.Web
 import Remote.List
+import Remote.List.Util
 import Config
 import Config.DynamicConfig
 import Git.Types (RemoteName, ConfigKey(..), fromConfigValue)
@@ -286,7 +287,7 @@ remoteFromUUID u = ifM ((==) u <$> getUUID)
 	findinmap = M.lookup u <$> remoteMap id
 	{- Re-read remote list in case a new remote has popped up. -}
 	tryharder = do
-		void remoteListRefresh
+		remotesChanged
 		findinmap
 
 {- Filters a list of remotes to ones that have the listed uuids. -}
diff --git a/Remote/List.hs b/Remote/List.hs
index e605a62cd1..db8c53feb5 100644
--- a/Remote/List.hs
+++ b/Remote/List.hs
@@ -21,7 +21,6 @@ import Remote.Helper.Hooks
 import Remote.Helper.ReadOnly
 import Remote.Helper.ExportImport
 import qualified Git
-import qualified Git.Config
 
 import qualified Remote.Git
 import qualified Remote.GCrypt
@@ -90,17 +89,6 @@ remoteList' autoinit = do
 		>>= mapM (remoteGen m t) 
 		>>= return . catMaybes
 
-{- Forces the remoteList to be re-generated, re-reading the git config. -}
-remoteListRefresh :: Annex [Remote]
-remoteListRefresh = do
-	newg <- inRepo Git.Config.reRead
-	Annex.changeState $ \s -> s 
-		{ Annex.remotes = []
-		, Annex.gitremotes = Nothing
-		, Annex.repo = newg
-		}
-	remoteList
-
 {- Generates a Remote. -}
 remoteGen :: M.Map UUID RemoteConfig -> RemoteType -> Git.Repo -> Annex (Maybe Remote)
 remoteGen m t g = do
diff --git a/Remote/List/Util.hs b/Remote/List/Util.hs
new file mode 100644
index 0000000000..382a98fa5d
--- /dev/null
+++ b/Remote/List/Util.hs
@@ -0,0 +1,24 @@
+{- git-annex remote list utils
+ -
+ - Copyright 2011-2020 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU AGPL version 3 or higher.
+ -}
+
+module Remote.List.Util where
+
+import Annex.Common
+import qualified Annex
+import qualified Git.Config
+
+{- Call when remotes have changed. Re-reads the git config, and
+ - invalidates the cache so the remoteList will be re-generated next time
+ - it's used. -}
+remotesChanged :: Annex ()
+remotesChanged = do
+	newg <- inRepo Git.Config.reRead
+	Annex.changeState $ \s -> s 
+		{ Annex.remotes = []
+		, Annex.gitremotes = Nothing
+		, Annex.repo = newg
+		}
diff --git a/doc/bugs/autoenable__61__true_seems_to_not_work_any_longer.mdwn b/doc/bugs/autoenable__61__true_seems_to_not_work_any_longer.mdwn
index b5396e7faf..021f9bf6d5 100644
--- a/doc/bugs/autoenable__61__true_seems_to_not_work_any_longer.mdwn
+++ b/doc/bugs/autoenable__61__true_seems_to_not_work_any_longer.mdwn
@@ -78,3 +78,5 @@ I am a little confused though since we do test for this scenario in datalad and
 [[!tag projects/datalad]]
 
 [[!meta title="autoenable not done for implicit init"]]
+
+> [[done]], autoinit will now autoenable --[[Joey]]
diff --git a/doc/git-annex-init.mdwn b/doc/git-annex-init.mdwn
index c6b814b277..2c48977e40 100644
--- a/doc/git-annex-init.mdwn
+++ b/doc/git-annex-init.mdwn
@@ -48,6 +48,11 @@ to the user who tries to run git-annex init.
   When the version given is one that automatically upgrades to a newer
   version, it will automatically use the newer version instead.
 
+* --autoenable
+
+  Only enable any special remotes that were configured with
+  autoenable=true, do not otherwise initialize anything.
+
 # SEE ALSO
 
 [[git-annex]](1)
diff --git a/doc/git-annex-initremote.mdwn b/doc/git-annex-initremote.mdwn
index ca204eac7f..c3fd0b0da0 100644
--- a/doc/git-annex-initremote.mdwn
+++ b/doc/git-annex-initremote.mdwn
@@ -93,10 +93,10 @@ want to use `git annex renameremote`.
 * `autoenable`
 
   To avoid `git annex enableremote` needing to be run,
-  you can pass "autoenable=true". Then when [[git-annex-init]](1)
-  is run in a new clone, it will attempt to enable the special remote. Of
-  course, this works best when the special remote does not need anything
-  special to be done to get it enabled.
+  you can pass "autoenable=true". Then when git-annex is run in a new clone,
+  it will attempt to enable the special remote. Of course, this works best
+  when the special remote does not need anything special to be done to get
+  it enabled.
 
 * `uuid`
 
diff --git a/git-annex.cabal b/git-annex.cabal
index d702fd81d6..9aa7430b18 100644
--- a/git-annex.cabal
+++ b/git-annex.cabal
@@ -956,6 +956,7 @@ Executable git-annex
     Remote.Helper.Ssh
     Remote.Hook
     Remote.List
+    Remote.List.Util
     Remote.P2P
     Remote.Rsync
     Remote.Rsync.RsyncUrl