diff --git a/fastmanifest/implementation.py b/fastmanifest/implementation.py
--- a/fastmanifest/implementation.py
+++ b/fastmanifest/implementation.py
@@ -1016,11 +1016,19 @@
         return node
 
     def ctxwrite(self, orig, mfctx, transaction, link, p1, p2, added, removed):
-        node = orig(mfctx, transaction, link, p1, p2, added, removed)
-
+        mfl = mfctx._manifestlog
         treeenabled = self.ui.configbool("fastmanifest", "usetree")
+        if (supportsctree and treeenabled and
+            p1 not in mfl._revlog.nodemap and
+            not mfl.datastore.getmissing([('', p1)])):
+            # If p1 is not in the flat manifest but is in the tree store, then
+            # this is a commit on top of a tree only commit and we should then
+            # produce a treeonly commit.
+            node = None
+        else:
+            node = orig(mfctx, transaction, link, p1, p2, added, removed)
+
         if supportsctree and treeenabled:
-            mfl = mfctx._manifestlog
             datastore = mfl.datastore
             opener = mfctx._revlog().opener
 
@@ -1082,13 +1090,25 @@
                     transaction.addabort('treepack', abort)
                     transaction.addpending('treepack', writepending)
 
-                dpack = treemanifest.InterceptedMutableDataPack(
-                        transaction.treedatapack,
-                        node, p1)
-                hpack = treemanifest.InterceptedMutableHistoryPack(
-                        transaction.treehistpack, node, p1)
+                # If the manifest was already committed as a flat manifest, use
+                # its node.
+                if node is not None:
+                    dpack = treemanifest.InterceptedMutableDataPack(
+                            transaction.treedatapack,
+                            node, p1)
+                    hpack = treemanifest.InterceptedMutableHistoryPack(
+                            transaction.treehistpack, node, p1)
+                else:
+                    dpack = transaction.treedatapack
+                    hpack = transaction.treehistpack
+
                 newtreeiter = newtree.finalize(tree)
                 for nname, nnode, ntext, np1text, np1, np2 in newtreeiter:
+                    # If the node wasn't set by a flat manifest, use the tree
+                    # root node.
+                    if node is None and nname == '':
+                        node = nnode
+
                     # Not using deltas, since there aren't any other trees in
                     # this pack it could delta against.
                     dpack.add(nname, nnode, revlog.nullid, ntext)
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
@@ -250,6 +250,28 @@
   |
   ~
 
+Test turning treeonly off and making sure we can still commit on top of treeonly
+commits
+  $ echo >> subdir/x
+  $ hg debugindex -m --config treemanifest.treeonly=False | tail -1
+       2       102      51     -1       2 0427baa4e948 85b359fdb09e 000000000000
+  $ hg commit -m 'treeonly from hybrid repo' --config treemanifest.treeonly=False
+  $ hg log -r . -T '{desc}\n' --stat
+  treeonly from hybrid repo
+   subdir/x |  1 +
+   1 files changed, 1 insertions(+), 0 deletions(-)
+  
+  $ hg log -r . -T '{desc}\n' --stat --config treemanifest.treeonly=False
+  treeonly from hybrid repo
+   subdir/x |  1 +
+   1 files changed, 1 insertions(+), 0 deletions(-)
+  
+  $ hg debugindex -m --config treemanifest.treeonly=False | tail -1
+       2       102      51     -1       2 0427baa4e948 85b359fdb09e 000000000000
+  $ hg strip -r . --config fbamend.safestrip=False
+  1 files updated, 0 files merged, 0 files removed, 0 files unresolved
+  saved backup bundle to $TESTTMP/client/.hg/strip-backup/87da9865954c-3cfa5389-backup.hg (glob)
+
 Test peer-to-peer push/pull of tree only commits
   $ cd ..
   $ clearcache