diff --git a/synapse/storage/devices.py b/synapse/storage/devices.py
index f0353929da..8e17800364 100644
--- a/synapse/storage/devices.py
+++ b/synapse/storage/devices.py
@@ -436,15 +436,27 @@ class DeviceStore(SQLBaseStore):
         )
 
     def _mark_as_sent_devices_by_remote_txn(self, txn, destination, stream_id):
+        # First we DELETE all rows such that only the latest row for each
+        # (destination, user_id is left. We do this by selecting first and
+        # deleting.
+        sql = """
+            SELECT user_id, coalesce(max(stream_id), 0) FROM device_lists_outbound_pokes
+            WHERE destination = ? AND stream_id <= ?
+            GROUP BY user_id
+            HAVING count(*) > 1
+        """
+        txn.execute(sql, (destination, stream_id,))
+        rows = txn.fetchall()
+
         sql = """
             DELETE FROM device_lists_outbound_pokes
-            WHERE destination = ? AND stream_id < (
-                SELECT coalesce(max(stream_id), 0) FROM device_lists_outbound_pokes
-                WHERE destination = ? AND stream_id <= ?
-            )
+            WHERE destination = ? AND user_id = ? AND stream_id < ?
         """
-        txn.execute(sql, (destination, destination, stream_id,))
+        txn.executemany(
+            sql, ((destination, row[0], row[1],) for row in rows)
+        )
 
+        # Mark everything that is left as sent
         sql = """
             UPDATE device_lists_outbound_pokes SET sent = ?
             WHERE destination = ? AND stream_id <= ?
@@ -545,18 +557,22 @@ class DeviceStore(SQLBaseStore):
         (destination, user_id) tuple to ensure that the prev_ids remain correct
         if the server does come back.
         """
-        now = self._clock.time_msec()
+        yesterday = self._clock.time_msec() - 24 * 60 * 60 * 1000
 
         def _prune_txn(txn):
             select_sql = """
                 SELECT destination, user_id, max(stream_id) as stream_id
                 FROM device_lists_outbound_pokes
                 GROUP BY destination, user_id
+                HAVING min(ts) < ? AND count(*) > 1
             """
 
-            txn.execute(select_sql)
+            txn.execute(select_sql, (yesterday,))
             rows = txn.fetchall()
 
+            if not rows:
+                return
+
             delete_sql = """
                 DELETE FROM device_lists_outbound_pokes
                 WHERE ts < ? AND destination = ? AND user_id = ? AND stream_id < ?
@@ -565,11 +581,13 @@ class DeviceStore(SQLBaseStore):
             txn.executemany(
                 delete_sql,
                 (
-                    (now, row["destination"], row["user_id"], row["stream_id"])
+                    (yesterday, row[0], row[1], row[2])
                     for row in rows
                 )
             )
 
+            logger.info("Pruned %d device list outbound pokes", txn.rowcount)
+
         return self.runInteraction(
             "_prune_old_outbound_device_pokes", _prune_txn
         )