diff --git a/hgext/mq.py b/hgext/mq.py
--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -66,6 +66,7 @@ from mercurial import commands, cmdutil,
 from mercurial import repair, extensions, error, phases
 from mercurial import patch as patchmod
 from mercurial import localrepo
+from mercurial import subrepo
 import os, re, errno, shutil
 
 commands.norepo += " qclone"
@@ -800,6 +801,14 @@ class queue(object):
                 p1, p2 = repo.dirstate.parents()
                 repo.setparents(p1, merge)
 
+            if all_files and '.hgsubstate' in all_files:
+                wctx = repo['.']
+                mctx = actx = repo[None]
+                overwrite = False
+                mergedsubstate = subrepo.submerge(repo, wctx, mctx, actx,
+                    overwrite)
+                files += mergedsubstate.keys()
+
             match = scmutil.matchfiles(repo, files or [])
             oldtip = repo['tip']
             n = newcommit(repo, None, message, ph.user, ph.date, match=match,
@@ -1459,6 +1468,8 @@ class queue(object):
                 self.ui.status(_("popping %s\n") % patch.name)
             del self.applied[start:end]
             self.strip(repo, [rev], update=False, backup='strip')
+            for s, state in repo['.'].substate.items():
+                repo['.'].sub(s).get(state)
             if self.applied:
                 self.ui.write(_("now at: %s\n") % self.applied[-1].name)
             else:
diff --git a/tests/test-mq-subrepo.t b/tests/test-mq-subrepo.t
--- a/tests/test-mq-subrepo.t
+++ b/tests/test-mq-subrepo.t
@@ -230,6 +230,8 @@ handle subrepos safely on qpush/qpop
   $ hg -R sub commit -m foo
   $ hg commit -m1
   $ hg qimport -r "0:tip"
+  $ hg -R sub id --id
+  aa037b301eba
 
 qpop
   $ hg -R sub update 0000
@@ -244,13 +246,11 @@ qpop
   popping 1.diff
   now at: 0.diff
   $ hg status -AS
-  M sub/a
   C .hgsub
   C .hgsubstate
-  $ hg debugsub
-  path sub
-   source   sub
-   revision b2fdb12cd82b021c3b7053d67802e77b6eeaee31
+  C sub/a
+  $ hg -R sub id --id
+  b2fdb12cd82b
 
 qpush
   $ hg -R sub update 0000
@@ -263,15 +263,14 @@ qpush
   adding sub/a
   $ hg qpush
   applying 1.diff
+  1 files updated, 0 files merged, 0 files removed, 0 files unresolved
   now at: 1.diff
   $ hg status -AS
-  M .hgsubstate
   C .hgsub
+  C .hgsubstate
   C sub/a
-  $ hg debugsub
-  path sub
-   source   sub
-   revision aa037b301eba54f350c75951b5486727fb98cbb5
+  $ hg -R sub id --id
+  aa037b301eba
 
   $ cd ..