diff --git a/changelog.d/13408.bugfix b/changelog.d/13408.bugfix
new file mode 100644
index 000000000000..8b87b2cf7be5
--- /dev/null
+++ b/changelog.d/13408.bugfix
@@ -0,0 +1 @@
+Fix a bug introduced in Synapse 1.57.0 where rooms listed in `exclude_rooms_from_sync` in the configuration file would not be properly excluded from incremental syncs.
diff --git a/synapse/handlers/sync.py b/synapse/handlers/sync.py
index d42a414c9040..d827c03ad187 100644
--- a/synapse/handlers/sync.py
+++ b/synapse/handlers/sync.py
@@ -1536,15 +1536,13 @@ async def _generate_sync_entry_for_rooms(
         ignored_users = await self.store.ignored_users(user_id)
         if since_token:
             room_changes = await self._get_rooms_changed(
-                sync_result_builder, ignored_users, self.rooms_to_exclude
+                sync_result_builder, ignored_users
             )
             tags_by_room = await self.store.get_updated_tags(
                 user_id, since_token.account_data_key
             )
         else:
-            room_changes = await self._get_all_rooms(
-                sync_result_builder, ignored_users, self.rooms_to_exclude
-            )
+            room_changes = await self._get_all_rooms(sync_result_builder, ignored_users)
             tags_by_room = await self.store.get_tags_for_user(user_id)
 
         log_kv({"rooms_changed": len(room_changes.room_entries)})
@@ -1623,13 +1621,14 @@ async def _get_rooms_changed(
         self,
         sync_result_builder: "SyncResultBuilder",
         ignored_users: FrozenSet[str],
-        excluded_rooms: List[str],
     ) -> _RoomChanges:
         """Determine the changes in rooms to report to the user.
 
         This function is a first pass at generating the rooms part of the sync response.
         It determines which rooms have changed during the sync period, and categorises
-        them into four buckets: "knock", "invite", "join" and "leave".
+        them into four buckets: "knock", "invite", "join" and "leave". It also excludes
+        from that list any room that appears in the list of rooms to exclude from sync
+        results in the server configuration.
 
         1. Finds all membership changes for the user in the sync period (from
            `since_token` up to `now_token`).
@@ -1655,7 +1654,7 @@ async def _get_rooms_changed(
         #       _have_rooms_changed. We could keep the results in memory to avoid a
         #       second query, at the cost of more complicated source code.
         membership_change_events = await self.store.get_membership_changes_for_user(
-            user_id, since_token.room_key, now_token.room_key, excluded_rooms
+            user_id, since_token.room_key, now_token.room_key, self.rooms_to_exclude
         )
 
         mem_change_events_by_room_id: Dict[str, List[EventBase]] = {}
@@ -1862,7 +1861,6 @@ async def _get_all_rooms(
         self,
         sync_result_builder: "SyncResultBuilder",
         ignored_users: FrozenSet[str],
-        ignored_rooms: List[str],
     ) -> _RoomChanges:
         """Returns entries for all rooms for the user.
 
@@ -1884,7 +1882,7 @@ async def _get_all_rooms(
         room_list = await self.store.get_rooms_for_local_user_where_membership_is(
             user_id=user_id,
             membership_list=Membership.LIST,
-            excluded_rooms=ignored_rooms,
+            excluded_rooms=self.rooms_to_exclude,
         )
 
         room_entries = []
@@ -2150,7 +2148,9 @@ async def _generate_room_entry(
                 raise Exception("Unrecognized rtype: %r", room_builder.rtype)
 
     async def get_rooms_for_user_at(
-        self, user_id: str, room_key: RoomStreamToken
+        self,
+        user_id: str,
+        room_key: RoomStreamToken,
     ) -> FrozenSet[str]:
         """Get set of joined rooms for a user at the given stream ordering.
 
@@ -2176,7 +2176,12 @@ async def get_rooms_for_user_at(
         # If the membership's stream ordering is after the given stream
         # ordering, we need to go and work out if the user was in the room
         # before.
+        # We also need to check whether the room should be excluded from sync
+        # responses as per the homeserver config.
         for joined_room in joined_rooms:
+            if joined_room.room_id in self.rooms_to_exclude:
+                continue
+
             if not joined_room.event_pos.persisted_after(room_key):
                 joined_room_ids.add(joined_room.room_id)
                 continue
diff --git a/tests/rest/client/test_sync.py b/tests/rest/client/test_sync.py
index b085c50356aa..ae161848281c 100644
--- a/tests/rest/client/test_sync.py
+++ b/tests/rest/client/test_sync.py
@@ -948,3 +948,24 @@ def test_invite(self) -> None:
 
         self.assertNotIn(self.excluded_room_id, channel.json_body["rooms"]["invite"])
         self.assertIn(self.included_room_id, channel.json_body["rooms"]["invite"])
+
+    def test_incremental_sync(self) -> None:
+        """Tests that activity in the room is properly filtered out of incremental
+        syncs.
+        """
+        channel = self.make_request("GET", "/sync", access_token=self.tok)
+        self.assertEqual(channel.code, 200, channel.result)
+        next_batch = channel.json_body["next_batch"]
+
+        self.helper.send(self.excluded_room_id, tok=self.tok)
+        self.helper.send(self.included_room_id, tok=self.tok)
+
+        channel = self.make_request(
+            "GET",
+            f"/sync?since={next_batch}",
+            access_token=self.tok,
+        )
+        self.assertEqual(channel.code, 200, channel.result)
+
+        self.assertNotIn(self.excluded_room_id, channel.json_body["rooms"]["join"])
+        self.assertIn(self.included_room_id, channel.json_body["rooms"]["join"])