diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
index 08fc9c1de..5e4ccafd2 100644
--- a/docs/CHANGELOG.rst
+++ b/docs/CHANGELOG.rst
@@ -22,6 +22,10 @@ Added
 - Add ``extend_lock`` method to redis cache in listener
 - Add extending processing lock task to the listener
 
+Changed
+-------
+- Wrap listener command processing in a transaction
+
 
 ===================
 38.1.0 - 2023-11-21
diff --git a/resolwe/flow/managers/listener/listener.py b/resolwe/flow/managers/listener/listener.py
index d3c9645d6..88a40540b 100644
--- a/resolwe/flow/managers/listener/listener.py
+++ b/resolwe/flow/managers/listener/listener.py
@@ -407,7 +407,8 @@ def process_command(self, identity: PeerIdentity, message: Message) -> Response:
 
         try:
             logger.debug(__("Invoking handler {}.", handler_name))
-            response = handler(data_id, message, self)
+            with transaction.atomic():
+                response = handler(data_id, message, self)
             # Check if data status was changed by the handler.
             if self.get_data_fields(data_id, "status") == Data.STATUS_ERROR:
                 response.status = ResponseStatus.ERROR