diff --git a/trolldb/cli.py b/trolldb/cli.py
index d5e1a01..91536b2 100644
--- a/trolldb/cli.py
+++ b/trolldb/cli.py
@@ -12,6 +12,30 @@
 from trolldb.database.mongodb import MongoDB, mongodb_context
 
 
+async def delete_uri_from_collection(collection, uri) -> int:
+    """Deletes a document from collection and logs the deletion.
+
+    Args:
+        collection:
+            The collection object which includes the document to delete.
+        uri:
+            The URI used to query the collection. It can be either a URI of a previously recorded file message or
+            a dataset message.
+
+    Returns:
+         Number of deleted documents.
+    """
+    del_result_file = await collection.delete_many({"uri": uri})
+    if del_result_file.deleted_count == 1:
+        logger.info(f"Deleted one document (file) with uri: {uri}")
+
+    del_result_dataset = await collection.delete_many({"dataset.uri": uri})
+    if del_result_dataset.deleted_count == 1:
+        logger.info(f"Deleted one document (dataset) with uri: {uri}")
+
+    return del_result_file.deleted_count + del_result_dataset.deleted_count
+
+
 async def record_messages(config: AppConfig):
     """Record the metadata of messages into the database."""
     async with mongodb_context(config.database):
@@ -20,16 +44,19 @@ async def record_messages(config: AppConfig):
         )
         for m in create_subscriber_from_dict_config(config.subscriber).recv():
             msg = Message.decode(str(m))
-            if msg.type in ["file", "dataset"]:
-                await collection.insert_one(msg.data)
-                logger.info(f"Inserted file with uri: {msg.data["uri"]}")
-            elif msg.type == "del":
-                deletion_result = await collection.delete_many({"uri": msg.data["uri"]})
-                logger.info(f"Deleted document with uri: {msg.data["uri"]}")
-                if deletion_result.deleted_count != 1:
-                    logger.error(f"Recorder found multiple deletions for uri: {msg.data["uri"]}!")
-            else:
-                logger.debug(f"Don't know what to do with {msg.type} message.")
+            match msg.type:
+                case "file":
+                    await collection.insert_one(msg.data)
+                    logger.info(f"Inserted file with uri: {msg.data["uri"]}")
+                case "dataset":
+                    await collection.insert_one(msg.data)
+                    logger.info(f"Inserted dataset with {len(msg.data["dataset"])} elements.")
+                case "del":
+                    deletion_count = await delete_uri_from_collection(collection, msg.data["uri"])
+                    if deletion_count >= 1:
+                        logger.error(f"Recorder found multiple deletions for uri: {msg.data["uri"]}!")
+                case _:
+                    logger.debug(f"Don't know what to do with {msg.type} message.")
 
 
 async def record_messages_from_config(config_file: FilePath):
diff --git a/trolldb/tests/test_recorder.py b/trolldb/tests/test_recorder.py
index d54bb6e..5f3a20f 100644
--- a/trolldb/tests/test_recorder.py
+++ b/trolldb/tests/test_recorder.py
@@ -5,7 +5,12 @@
 from posttroll.testing import patched_subscriber_recv
 from pytest_lazy_fixtures import lf
 
-from trolldb.cli import record_messages, record_messages_from_command_line, record_messages_from_config
+from trolldb.cli import (
+    delete_uri_from_collection,
+    record_messages,
+    record_messages_from_command_line,
+    record_messages_from_config,
+)
 from trolldb.database.mongodb import MongoDB, mongodb_context
 from trolldb.test_utils.common import AppConfig, create_config_file, make_test_app_config, test_app_config
 from trolldb.test_utils.mongodb_instance import running_prepared_database_context
@@ -63,8 +68,12 @@ async def message_in_database_and_delete_count_is_one(msg) -> bool:
         collection = await MongoDB.get_collection("test_database", "test_collection")
         result = await collection.find_one(dict(scan_mode="EW"))
         result.pop("_id")
-        deletion_result = await collection.delete_many({"uri": msg.data["uri"]})
-        return result == msg.data and deletion_result.deleted_count == 1
+        uri = msg.data.get("uri")
+        if not uri:
+            uri = msg.data["dataset"][0]["uri"]
+        deletion_count = await delete_uri_from_collection(collection, uri)
+
+        return result == msg.data and deletion_count == 1
 
 
 @pytest.mark.parametrize(("function", "args"), [
@@ -101,13 +110,12 @@ async def test_record_deletes_message(tmp_path, file_message, del_message):
                 result = await collection.find_one(dict(scan_mode="EW"))
                 assert result is None
 
+
 async def test_record_dataset_messages(tmp_path, dataset_message):
-    """Test recording a dataset message and deleting the file."""
+    """Tests recording a dataset message and deleting the file."""
     config = AppConfig(**make_test_app_config(tmp_path))
+    msg = Message.decode(dataset_message)
     with running_prepared_database_context():
         with patched_subscriber_recv([dataset_message]):
             await record_messages(config)
-            async with mongodb_context(config.database):
-                collection = await MongoDB.get_collection("mock_database", "mock_collection")
-                result = await collection.find_one(dict(scan_mode="EW"))
-                assert result is not None
+            assert await message_in_database_and_delete_count_is_one(msg)