diff --git a/synapse/handlers/federation.py b/synapse/handlers/federation.py
index 65cfacba2e..15ba417e06 100644
--- a/synapse/handlers/federation.py
+++ b/synapse/handlers/federation.py
@@ -290,6 +290,8 @@ class FederationHandler(BaseHandler):
         """
         logger.debug("Joining %s to %s", joinee, room_id)
 
+        yield self.store.clean_room_for_join(room_id)
+
         origin, pdu = yield self.replication_layer.make_join(
             target_hosts,
             room_id,
diff --git a/synapse/storage/event_federation.py b/synapse/storage/event_federation.py
index 2deda8ac50..032334bfd6 100644
--- a/synapse/storage/event_federation.py
+++ b/synapse/storage/event_federation.py
@@ -429,3 +429,15 @@ class EventFederationStore(SQLBaseStore):
         )
 
         return events[:limit]
+
+    def clean_room_for_join(self, room_id):
+        return self.runInteraction(
+            "clean_room_for_join",
+            self._clean_room_for_join_txn,
+            room_id,
+        )
+
+    def _clean_room_for_join_txn(self, txn, room_id):
+        query = "DELETE FROM event_forward_extremities WHERE room_id = ?"
+
+        txn.execute(query, (room_id,))