diff --git a/mercurial/upgrade_utils/engine.py b/mercurial/upgrade_utils/engine.py
--- a/mercurial/upgrade_utils/engine.py
+++ b/mercurial/upgrade_utils/engine.py
@@ -468,6 +468,13 @@
             unfi = srcrepo.unfiltered()
             cl = unfi.changelog
             nodemap.persist_nodemap(tr, cl, force=True)
+            # we want to directly operate on the underlying revlog to force
+            # create a nodemap file. This is fine since this is upgrade code
+            # and it heavily relies on repository being revlog based
+            # hence accessing private attributes can be justified
+            nodemap.persist_nodemap(
+                tr, unfi.manifestlog._rootstore._revlog, force=True
+            )
         scmutil.writereporequirements(srcrepo, upgrade_op.new_requirements)
     else:
         with dstrepo.transaction(b'upgrade') as tr:
diff --git a/tests/test-persistent-nodemap.t b/tests/test-persistent-nodemap.t
--- a/tests/test-persistent-nodemap.t
+++ b/tests/test-persistent-nodemap.t
@@ -641,6 +641,8 @@
   $ ls -1 .hg/store/ | egrep '00(changelog|manifest)(\.n|-.*\.nd)'
   00changelog-*.nd (glob)
   00changelog.n
+  00manifest-*.nd (glob)
+  00manifest.n
 
   $ hg debugnodemap --metadata
   uid: * (glob)