diff --git a/remotefilelog/__init__.py b/remotefilelog/__init__.py
--- a/remotefilelog/__init__.py
+++ b/remotefilelog/__init__.py
@@ -163,6 +163,8 @@
                         opts['includepattern'] = '\0'.join(repo.includepattern)
                     if repo.excludepattern:
                         opts['excludepattern'] = '\0'.join(repo.excludepattern)
+                    if repo.ui.configbool("treemanifest", "treeonly"):
+                        opts['noflatmanifest'] = 'True'
                     return remote._callstream('stream_out_shallow', **opts)
                 else:
                     return orig()
diff --git a/remotefilelog/remotefilelogserver.py b/remotefilelog/remotefilelogserver.py
--- a/remotefilelog/remotefilelogserver.py
+++ b/remotefilelog/remotefilelogserver.py
@@ -74,6 +74,7 @@
     class streamstate(object):
         match = None
         shallowremote = False
+        noflatmf = False
     state = streamstate()
 
     def stream_out_shallow(repo, proto, other):
@@ -88,9 +89,11 @@
 
         oldshallow = state.shallowremote
         oldmatch = state.match
+        oldnoflatmf = state.noflatmf
         try:
             state.shallowremote = True
             state.match = match.always(repo.root, '')
+            state.noflatmf = other.get('noflatmanifest') == 'True'
             if includepattern or excludepattern:
                 state.match = match.match(repo.root, '', None,
                     includepattern, excludepattern)
@@ -109,6 +112,7 @@
         finally:
             state.shallowremote = oldshallow
             state.match = oldmatch
+            state.noflatmf = oldnoflatmf
 
     wireproto.commands['stream_out_shallow'] = (stream_out_shallow, '*')
 
@@ -150,6 +154,8 @@
             for x in repo.store.topfiles():
                 if shallowtrees and x[0][:15] == '00manifesttree.':
                     continue
+                if state.noflatmf and x[0][:11] == '00manifest.':
+                    continue
                 yield x
 
         elif shallowrepo.requirement in repo.requirements:
diff --git a/tests/test-treemanifest-treeonly.t b/tests/test-treemanifest-treeonly.t
--- a/tests/test-treemanifest-treeonly.t
+++ b/tests/test-treemanifest-treeonly.t
@@ -16,6 +16,7 @@
   > server=True
   > [remotefilelog]
   > server=True
+  > shallowtrees=True
   > EOF
 
 Make local commits on the server
@@ -251,10 +252,18 @@
 Test peer-to-peer push/pull of tree only commits
   $ cd ..
   $ clearcache
-# TODO: Test tree only clone
-  $ hgcloneshallow ssh://user@dummy/master client2 -q
+  $ hgcloneshallow ssh://user@dummy/master client2 -q --config treemanifest.treeonly=True --config extensions.treemanifest=
+  2 trees fetched over * (glob)
+  1 trees fetched over * (glob)
   1 files fetched over 1 fetches - (1 misses, 0.00% hit ratio) over * (glob)
   $ cd client2
+  $ ls_l .hg/store
+  -rw-r--r--     277 00changelog.i
+  drwxr-xr-x         data
+  -rw-r--r--       0 undo
+  -rw-r--r--       2 undo.backupfiles
+  -rw-r--r--       0 undo.phaseroots
+  $ rm -rf $CACHEDIR
   $ cp ../client/.hg/hgrc .hg/hgrc
 
 # Test pulling from a treeonly peer