diff --git a/changelog.d/unreferenced-state-groups-order.bugfix b/changelog.d/unreferenced-state-groups-order.bugfix
new file mode 100644
index 0000000000..6051027072
--- /dev/null
+++ b/changelog.d/unreferenced-state-groups-order.bugfix
@@ -0,0 +1 @@
+Fix unreferenced state groups sometimes not being marked for deletion, depending on the order the database returned rows in.
diff --git a/synapse/storage/controllers/purge_events.py b/synapse/storage/controllers/purge_events.py
index 8a2053d25a..e461114fcd 100644
--- a/synapse/storage/controllers/purge_events.py
+++ b/synapse/storage/controllers/purge_events.py
@@ -374,6 +374,7 @@ class PurgeEventsStorageController:
                 ) as s
                 LEFT JOIN state_group_edges AS e ON (s.id = e.prev_state_group)
                 LEFT JOIN state_groups_pending_deletion AS d ON (e.state_group = d.state_group)
+                ORDER BY s.id DESC
             """
             txn.execute(state_group_sql, (last_checked_state_group, batch_size))