--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -417,6 +417,7 @@ class queue:
                 self.applied_dirty = 1
             if err:
                 return (err, head)
+        self.save_dirty()
         return (0, head)
 
     def patch(self, repo, patchfile):

--- a/tests/test-mq-merge
+++ b/tests/test-mq-merge
@@ -37,3 +37,6 @@ hg ci -m update
 hg manifest
 hg qpush -a -m 2>&1 | rewrite_path
 hg manifest
+
+# ensure status is correct after merge
+hg qpop -a

--- a/tests/test-mq-merge.out
+++ b/tests/test-mq-merge.out
@@ -9,3 +9,4 @@ merging with queue at: .hg/patches.1
 applying rm_a
 Now at: rm_a
 b
+Patch queue now empty