diff --git a/eden/scm/edenscm/mercurial/store.py b/eden/scm/edenscm/mercurial/store.py
index d4fddb13ec..9c3511336b 100644
--- a/eden/scm/edenscm/mercurial/store.py
+++ b/eden/scm/edenscm/mercurial/store.py
@@ -588,13 +588,21 @@ class metavfs(object):
         vfs = self.vfs
         metalog = bindings.metalog.metalog(vfs.join("metalog"))
 
-        # Migrate data from vfs to metalog
-        keys = set(metalog.keys())
-        for name in self.metapaths:
-            if name not in keys:
-                data = vfs.tryread(name)
-                if data is not None:
-                    metalog[name] = data
+        # Keys that are previously tracked in metalog.
+        tracked = set((metalog.get("tracked") or "").split())
+        # Keys that should be tracked (specified by config).
+        desired = set(self.metapaths)
+
+        # Migrate up (from svfs plain files to metalog).
+        for name in desired.difference(tracked):
+            data = vfs.tryread(name)
+            if data is not None:
+                metalog[name] = data
+
+        # Migrating down is a no-op, since we double-write to svfs too.
+
+        metalog["tracked"] = "\n".join(sorted(desired))
+
         try:
             # XXX: This is racy.
             metalog.commit("migrate from vfs", int(util.timer()))
diff --git a/eden/scm/tests/test-metalog-migration-t.py b/eden/scm/tests/test-metalog-migration-t.py
new file mode 100644
index 0000000000..67882c6393
--- /dev/null
+++ b/eden/scm/tests/test-metalog-migration-t.py
@@ -0,0 +1,84 @@
+# Copyright (c) Facebook, Inc. and its affiliates.
+#
+# This software may be used and distributed according to the terms of the
+# GNU General Public License version 2.
+
+from __future__ import absolute_import
+
+from testutil.autofix import eq
+from testutil.dott import feature, sh, testtmp  # noqa: F401
+
+
+def backup():
+    """Backup .hg/store/{bookmarks,remotenames}"""
+    for name in ["bookmarks", "remotenames"]:
+        path = ".hg/store/%s" % name
+        sh.cp(path, "%s.bak" % path)
+
+
+def restore():
+    """Rewrite .hg/store/{bookmarks,remotenames} with backup"""
+    for name in ["bookmarks", "remotenames"]:
+        path = ".hg/store/%s" % name
+        sh.cp("%s.bak" % path, path)
+
+
+def setbookmarks(name):
+    """Set bookmarks to specified commit"""
+    sh.hg("bookmark", "book", "-r", "desc(%s)" % name)
+    sh.hg("debugremotebookmark", "remotebook", "desc(%s)" % name)
+
+
+def listbookmarks():
+    """List local and remote bookmarks"""
+    local = sh.hg("log", "-r", sh.hg("bookmarks", "-T", "{node}"), "-T{desc}")
+    remote = sh.hg(
+        "log", "-r", sh.hg("bookmarks", "--remote", "-T", "{node}"), "-T{desc}"
+    )
+    return [local, remote]
+
+
+sh.newrepo()
+sh.setconfig("experimental.metalog=0")
+sh.enable("remotenames")
+
+sh % "drawdag" << r"""
+C
+|
+B
+|
+A
+"""
+
+# Prepare bookmarks and remotenames. Set them to A in backup, and B on disk.
+
+setbookmarks("A")
+backup()
+setbookmarks("B")
+
+# Test migrating from disk to metalog.
+# They should migrate "B" from disk to metalog and use it.
+
+sh.setconfig("experimental.metalog=1")
+eq(listbookmarks(), ["B", "B"])
+
+# Metalog is the source of truth. Changes to .hg/store are ignored.
+
+restore()
+eq(listbookmarks(), ["B", "B"])
+
+# Test migrating from metalog to disk.
+# Metalog is not the source of truth. Changes to .hg/store are effective.
+
+sh.setconfig("experimental.metalog=0")
+setbookmarks("C")
+eq(listbookmarks(), ["C", "C"])
+restore()
+eq(listbookmarks(), ["A", "A"])
+
+# Migrate up again.
+# At this time metalog should import "A" from disk to metalog, instead of
+# using "B" that exists in metalog.
+
+sh.setconfig("experimental.metalog=1")
+eq(listbookmarks(), ["A", "A"])