diff --git a/changelog.d/6310.feature b/changelog.d/6310.feature
new file mode 100644
index 0000000000..78a187a1dc
--- /dev/null
+++ b/changelog.d/6310.feature
@@ -0,0 +1 @@
+Implement label-based filtering on `/sync` and `/messages` ([MSC2326](https://github.com/matrix-org/matrix-doc/pull/2326)).
diff --git a/synapse/storage/data_stores/main/events_bg_updates.py b/synapse/storage/data_stores/main/events_bg_updates.py
index 51352b9966..0ed59ef48e 100644
--- a/synapse/storage/data_stores/main/events_bg_updates.py
+++ b/synapse/storage/data_stores/main/events_bg_updates.py
@@ -21,6 +21,7 @@ from canonicaljson import json
 
 from twisted.internet import defer
 
+from synapse.api.constants import EventContentFields
 from synapse.storage._base import make_in_list_sql_clause
 from synapse.storage.background_updates import BackgroundUpdateStore
 
@@ -85,6 +86,10 @@ class EventsBackgroundUpdatesStore(BackgroundUpdateStore):
             "event_fix_redactions_bytes", self._event_fix_redactions_bytes
         )
 
+        self.register_background_update_handler(
+            "event_store_labels", self._event_store_labels
+        )
+
     @defer.inlineCallbacks
     def _background_reindex_fields_sender(self, progress, batch_size):
         target_min_stream_id = progress["target_min_stream_id_inclusive"]
@@ -503,3 +508,61 @@ class EventsBackgroundUpdatesStore(BackgroundUpdateStore):
         yield self._end_background_update("event_fix_redactions_bytes")
 
         return 1
+
+    @defer.inlineCallbacks
+    def _event_store_labels(self, progress, batch_size):
+        """Background update handler which will store labels for existing events."""
+        last_event_id = progress.get("last_event_id", "")
+
+        def _event_store_labels_txn(txn):
+            txn.execute(
+                """
+                SELECT event_id, json FROM event_json
+                LEFT JOIN event_labels USING (event_id)
+                WHERE event_id > ? AND label IS NULL
+                ORDER BY event_id LIMIT ?
+                """,
+                (last_event_id, batch_size),
+            )
+
+            results = list(txn)
+
+            nbrows = 0
+            last_row_event_id = ""
+            for (event_id, event_json_raw) in results:
+                event_json = json.loads(event_json_raw)
+
+                self._simple_insert_many_txn(
+                    txn=txn,
+                    table="event_labels",
+                    values=[
+                        {
+                            "event_id": event_id,
+                            "label": label,
+                            "room_id": event_json["room_id"],
+                            "topological_ordering": event_json["depth"],
+                        }
+                        for label in event_json["content"].get(
+                            EventContentFields.LABELS, []
+                        )
+                        if isinstance(label, str)
+                    ],
+                )
+
+                nbrows += 1
+                last_row_event_id = event_id
+
+            self._background_update_progress_txn(
+                txn, "event_store_labels", {"last_event_id": last_row_event_id}
+            )
+
+            return nbrows
+
+        num_rows = yield self.runInteraction(
+            desc="event_store_labels", func=_event_store_labels_txn
+        )
+
+        if not num_rows:
+            yield self._end_background_update("event_store_labels")
+
+        return num_rows
diff --git a/synapse/storage/data_stores/main/schema/delta/56/event_labels_background_update.sql b/synapse/storage/data_stores/main/schema/delta/56/event_labels_background_update.sql
new file mode 100644
index 0000000000..5f5e0499ae
--- /dev/null
+++ b/synapse/storage/data_stores/main/schema/delta/56/event_labels_background_update.sql
@@ -0,0 +1,17 @@
+/* Copyright 2019 The Matrix.org Foundation C.I.C.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+INSERT INTO background_updates (update_name, progress_json) VALUES
+  ('event_store_labels', '{}');