diff --git a/changelog.d/6092.bugfix b/changelog.d/6092.bugfix
new file mode 100644
index 000000000000..01a7498ec6b4
--- /dev/null
+++ b/changelog.d/6092.bugfix
@@ -0,0 +1 @@
+Fix the logged number of updated items for the users_set_deactivated_flag background update.
diff --git a/synapse/storage/background_updates.py b/synapse/storage/background_updates.py
index e5f0668f0909..9522acd972c9 100644
--- a/synapse/storage/background_updates.py
+++ b/synapse/storage/background_updates.py
@@ -218,7 +218,7 @@ def _do_background_update(self, update_name, desired_duration_ms):
         duration_ms = time_stop - time_start
 
         logger.info(
-            "Updating %r. Updated %r items in %rms."
+            "Running background update %r. Processed %r items in %rms."
             " (total_rate=%r/ms, current_rate=%r/ms, total_updated=%r, batch_size=%r)",
             update_name,
             items_updated,
diff --git a/synapse/storage/registration.py b/synapse/storage/registration.py
index 805411a6b299..c3acc8ecafbb 100644
--- a/synapse/storage/registration.py
+++ b/synapse/storage/registration.py
@@ -844,7 +844,7 @@ def _background_update_set_deactivated_flag_txn(txn):
             rows = self.cursor_to_dict(txn)
 
             if not rows:
-                return True
+                return True, 0
 
             rows_processed_nb = 0
 
@@ -860,18 +860,18 @@ def _background_update_set_deactivated_flag_txn(txn):
             )
 
             if batch_size > len(rows):
-                return True
+                return True, len(rows)
             else:
-                return False
+                return False, len(rows)
 
-        end = yield self.runInteraction(
+        end, nb_processed = yield self.runInteraction(
             "users_set_deactivated_flag", _background_update_set_deactivated_flag_txn
         )
 
         if end:
             yield self._end_background_update("users_set_deactivated_flag")
 
-        return batch_size
+        return nb_processed
 
     @defer.inlineCallbacks
     def add_access_token_to_user(self, user_id, token, device_id, valid_until_ms):