diff --git a/changelog.d/11420.bugfix b/changelog.d/11420.bugfix
new file mode 100644
index 000000000000..94cf73e03da9
--- /dev/null
+++ b/changelog.d/11420.bugfix
@@ -0,0 +1 @@
+Improve performance of various background updates related to device inboxes.
diff --git a/synapse/storage/databases/main/deviceinbox.py b/synapse/storage/databases/main/deviceinbox.py
index 7c0f95336561..855d199f2ac8 100644
--- a/synapse/storage/databases/main/deviceinbox.py
+++ b/synapse/storage/databases/main/deviceinbox.py
@@ -737,31 +737,28 @@ async def _remove_hidden_devices_from_device_inbox(
         def _remove_hidden_devices_from_device_inbox_txn(
             txn: LoggingTransaction,
         ) -> int:
-            """stream_id is not unique
-            we need to use an inclusive `stream_id >= ?` clause,
-            since we might not have deleted all hidden device messages for the stream_id
-            returned from the previous query
+            """Retrieve the list of hidden devices that appear in the device_inbox table,
+            ordered by user_id so the query uses the index on the devices table.
 
             Then delete only rows matching the `(user_id, device_id, stream_id)` tuple,
             to avoid problems of deleting a large number of rows all at once
             due to a single device having lots of device messages.
             """
 
-            last_stream_id = progress.get("stream_id", 0)
+            last_user_id = progress.get("mxid", "")
 
             sql = """
                 SELECT device_id, user_id, stream_id
-                FROM device_inbox
+                FROM devices
+                INNER JOIN device_inbox USING (device_id, user_id)
                 WHERE
-                    stream_id >= ?
-                    AND (device_id, user_id) IN (
-                        SELECT device_id, user_id FROM devices WHERE hidden = ?
-                    )
-                ORDER BY stream_id
+                    user_id >= ?
+                    AND hidden = ?
+                ORDER BY user_id
                 LIMIT ?
             """
 
-            txn.execute(sql, (last_stream_id, True, batch_size))
+            txn.execute(sql, (last_user_id, True, batch_size))
             rows = txn.fetchall()
 
             num_deleted = 0
@@ -782,7 +779,7 @@ def _remove_hidden_devices_from_device_inbox_txn(
                     self.REMOVE_HIDDEN_DEVICES,
                     {
                         "device_id": rows[-1][0],
-                        "user_id": rows[-1][1],
+                        "mxid": rows[-1][1],
                         "stream_id": rows[-1][2],
                     },
                 )