diff --git a/src/ert/config/queue_config.py b/src/ert/config/queue_config.py
index 6900cbb882e..f5c5a0f6c76 100644
--- a/src/ert/config/queue_config.py
+++ b/src/ert/config/queue_config.py
@@ -3,13 +3,14 @@
 import logging
 import re
 import shutil
+import warnings
 from collections import defaultdict
 from dataclasses import dataclass, field
 from typing import Any, Dict, List, Mapping, Tuple, no_type_check
 
 from ert import _clib
 
-from .parsing import ConfigDict, ConfigValidationError
+from .parsing import ConfigDict, ConfigValidationError, ConfigWarning
 from .queue_system import QueueSystem
 
 GENERIC_QUEUE_OPTIONS: List[str] = ["MAX_RUNNING"]
@@ -58,6 +59,15 @@ def from_dict(cls, config_dict: ConfigDict) -> QueueConfig:
                     f"Invalid QUEUE_OPTION for {queue_system.name}: '{option_name}'. "
                     f"Valid choices are {sorted(VALID_QUEUE_OPTIONS[queue_system])}."
                 )
+            if queue_system != selected_queue_system:
+                warnings.warn(
+                    ConfigWarning.with_context(
+                        f"Setting '{option_name}'for {queue_system.name} but "
+                        f"{selected_queue_system.name} is selected. ",
+                        option_name,
+                    ),
+                    stacklevel=1,
+                )
             queue_options[queue_system].append(
                 (option_name, values[0] if values else "")
             )