diff --git a/scripts/_helpers.py b/scripts/_helpers.py
index 73de2f92c..5babccaae 100644
--- a/scripts/_helpers.py
+++ b/scripts/_helpers.py
@@ -175,7 +175,22 @@ def path_provider(dir, rdir, shared_resources, exclude_from_shared):
     )
 
 
-def check_deprecated_config(config: dict, deprecations_file: str) -> None:
+def _check_scenarios(config: dict, check_fn: Callable, fn_kwargs: dict) -> None:
+    """Helper function to check configuration in scenario files"""
+    scenarios = config.get("run", {}).get("scenarios", {})
+    if scenarios.get("enable"):
+        with open(scenarios["file"]) as f:
+            scenario_config = yaml.safe_load(f)
+
+        for run in scenario_config:
+            # Disable recursive scenario checking to avoid infinite loops
+            fn_kwargs["check_scenarios"] = False
+            check_fn(scenario_config[run], **fn_kwargs)
+
+
+def check_deprecated_config(
+    config: dict, deprecations_file: str, check_scenarios: bool = True
+) -> None:
     """Check config against deprecations and warn users"""
 
     with open(deprecations_file) as f:
@@ -219,8 +234,15 @@ def set_by_path(root, path, value):
 
             warnings.warn(msg, DeprecationConfigWarning)
 
+    if check_scenarios:
+        _check_scenarios(
+            config, check_deprecated_config, {"deprecations_file": deprecations_file}
+        )
+
 
-def check_invalid_config(config: dict, config_default_fn: str) -> None:
+def check_invalid_config(
+    config: dict, config_default_fn: str, check_scenarios: bool = True
+) -> None:
     """Check if config contains entries that are not supported by the default config"""
 
     with open(config_default_fn) as f:
@@ -241,6 +263,11 @@ def check_keys(config, config_default, path=""):
 
     check_keys(config, config_default)
 
+    if check_scenarios:
+        _check_scenarios(
+            config, check_invalid_config, {"config_default_fn": config_default_fn}
+        )
+
 
 def get_opt(opts, expr, flags=None):
     """
diff --git a/test/test_config_checks.py b/test/test_config_checks.py
index f0384334d..e18ee3bdf 100644
--- a/test/test_config_checks.py
+++ b/test/test_config_checks.py
@@ -22,6 +22,22 @@
 - old_entry: "example:old_key"
   new_entry: "example:new_key"
   message: "Custom warning message"
+
+- old_entry: "clustering:deprecated_option"
+  message: "Custom warning message for deprecated clustering option"
+"""
+
+SAMPLE_SCENARIOS = """
+scenario_1:
+    example:
+        old_key: "test_value"
+    invalid_section:
+        some_key: "value"
+
+scenario_2:
+    clustering:
+        invalid_option: "bad"
+        deprecated_option: "old_value"
 """
 
 
@@ -107,3 +123,63 @@ def test_config_invalid_entries():
 
     # Verify warning types
     assert all(isinstance(w.message, InvalidConfigWarning) for w in captured_warnings)
+
+
+def test_config_scenario_checks():
+    """Test that configuration checks are performed on scenario files"""
+    config = {
+        "run": {
+            "scenarios": {
+                "enable": True,
+                "file": "scenarios.yaml",
+            }
+        }
+    }
+
+    # Setup mock files
+    mock_files = {
+        "deprecations.yaml": SAMPLE_DEPRECATIONS,
+        "config.default.yaml": """
+            run:
+              scenarios:
+                  enable: true
+                  file: scenarios.yaml
+            example:
+                new_key: "default"
+            clustering:
+                temporal:
+                    resolution: 1
+            """,
+        "scenarios.yaml": SAMPLE_SCENARIOS,
+    }
+
+    def mock_open(filename, *args, **kwargs):
+        return StringIO(mock_files[filename.split("/")[-1]])
+
+    with warnings.catch_warnings(record=True) as captured_warnings:
+        with patch("builtins.open", mock_open):
+            # Check both deprecated and invalid entries in scenarios
+            check_deprecated_config(config, "deprecations.yaml")
+            check_invalid_config(config, "config.default.yaml")
+
+    warning_messages = [str(w.message) for w in captured_warnings]
+
+    # Verify warnings from scenario_1
+    assert any("'example:old_key' is deprecated" in msg for msg in warning_messages)
+    assert any("'invalid_section' is not supported" in msg for msg in warning_messages)
+
+    # Verify warnings from scenario_2
+    assert any(
+        "'clustering:invalid_option' is not supported" in msg
+        for msg in warning_messages
+    )
+
+    # Verify warning types
+    deprecation_warnings = [
+        w for w in captured_warnings if isinstance(w.message, DeprecationConfigWarning)
+    ]
+    invalid_warnings = [
+        w for w in captured_warnings if isinstance(w.message, InvalidConfigWarning)
+    ]
+    assert len(deprecation_warnings) == 2
+    assert len(invalid_warnings) == 4