diff --git a/changelog.d/14181.bugfix b/changelog.d/14181.bugfix
new file mode 100644
index 000000000..36521c670
--- /dev/null
+++ b/changelog.d/14181.bugfix
@@ -0,0 +1 @@
+Fix poor performance of the `event_push_backfill_thread_id` background update, which was introduced in Synapse 1.68.0rc1.
diff --git a/synapse/storage/databases/main/event_push_actions.py b/synapse/storage/databases/main/event_push_actions.py
index 7f7bcb709..72cf91eb3 100644
--- a/synapse/storage/databases/main/event_push_actions.py
+++ b/synapse/storage/databases/main/event_push_actions.py
@@ -269,11 +269,11 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
         event_push_actions_done = progress.get("event_push_actions_done", False)
 
         def add_thread_id_txn(
-            txn: LoggingTransaction, table_name: str, start_stream_ordering: int
+            txn: LoggingTransaction, start_stream_ordering: int
         ) -> int:
-            sql = f"""
+            sql = """
             SELECT stream_ordering
-            FROM {table_name}
+            FROM event_push_actions
             WHERE
                 thread_id IS NULL
                 AND stream_ordering > ?
@@ -285,7 +285,7 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             # No more rows to process.
             rows = txn.fetchall()
             if not rows:
-                progress[f"{table_name}_done"] = True
+                progress["event_push_actions_done"] = True
                 self.db_pool.updates._background_update_progress_txn(
                     txn, "event_push_backfill_thread_id", progress
                 )
@@ -294,8 +294,8 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             # Update the thread ID for any of those rows.
             max_stream_ordering = rows[-1][0]
 
-            sql = f"""
-            UPDATE {table_name}
+            sql = """
+            UPDATE event_push_actions
             SET thread_id = 'main'
             WHERE ? < stream_ordering AND stream_ordering <= ? AND thread_id IS NULL
             """
@@ -309,7 +309,50 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
 
             # Update progress.
             processed_rows = txn.rowcount
-            progress[f"max_{table_name}_stream_ordering"] = max_stream_ordering
+            progress["max_event_push_actions_stream_ordering"] = max_stream_ordering
+            self.db_pool.updates._background_update_progress_txn(
+                txn, "event_push_backfill_thread_id", progress
+            )
+
+            return processed_rows
+
+        def add_thread_id_summary_txn(txn: LoggingTransaction) -> int:
+            min_user_id = progress.get("max_summary_user_id", "")
+            min_room_id = progress.get("max_summary_room_id", "")
+
+            # Slightly overcomplicated query for getting the Nth user ID / room
+            # ID tuple, or the last if there are less than N remaining.
+            sql = """
+            SELECT user_id, room_id FROM (
+                SELECT user_id, room_id FROM event_push_summary
+                WHERE (user_id, room_id) > (?, ?)
+                    AND thread_id IS NULL
+                ORDER BY user_id, room_id
+                LIMIT ?
+            ) AS e
+            ORDER BY user_id DESC, room_id DESC
+            LIMIT 1
+            """
+
+            txn.execute(sql, (min_user_id, min_room_id, batch_size))
+            row = txn.fetchone()
+            if not row:
+                return 0
+
+            max_user_id, max_room_id = row
+
+            sql = """
+            UPDATE event_push_summary
+            SET thread_id = 'main'
+            WHERE
+                (?, ?) < (user_id, room_id) AND (user_id, room_id) <= (?, ?)
+                AND thread_id IS NULL
+            """
+            txn.execute(sql, (min_user_id, min_room_id, max_user_id, max_room_id))
+            processed_rows = txn.rowcount
+
+            progress["max_summary_user_id"] = max_user_id
+            progress["max_summary_room_id"] = max_room_id
             self.db_pool.updates._background_update_progress_txn(
                 txn, "event_push_backfill_thread_id", progress
             )
@@ -325,15 +368,12 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             result = await self.db_pool.runInteraction(
                 "event_push_backfill_thread_id",
                 add_thread_id_txn,
-                "event_push_actions",
                 progress.get("max_event_push_actions_stream_ordering", 0),
             )
         else:
             result = await self.db_pool.runInteraction(
                 "event_push_backfill_thread_id",
-                add_thread_id_txn,
-                "event_push_summary",
-                progress.get("max_event_push_summary_stream_ordering", 0),
+                add_thread_id_summary_txn,
             )
 
             # Only done after the event_push_summary table is done.