diff --git a/synapse/handlers/deactivate_account.py b/synapse/handlers/deactivate_account.py
index b8cf6ab57c..3d86ef1c49 100644
--- a/synapse/handlers/deactivate_account.py
+++ b/synapse/handlers/deactivate_account.py
@@ -121,6 +121,9 @@ class DeactivateAccountHandler(BaseHandler):
         # parts users from rooms (if it isn't already running)
         self._start_user_parting()
 
+        # Mark the user as deactivated.
+        yield self.store.set_user_deactivated_status(user_id, True)
+
         # Remove all information on the user from the account_validity table.
         if self._account_validity_enabled:
             yield self.store.delete_account_validity_for_user(user_id)