diff --git a/src/openflexure_microscope_server/server/__init__.py b/src/openflexure_microscope_server/server/__init__.py
index 3735f312..01028715 100644
--- a/src/openflexure_microscope_server/server/__init__.py
+++ b/src/openflexure_microscope_server/server/__init__.py
@@ -72,7 +72,7 @@ def set_shutdown_function(shutdown_function: Callable[[], None]) -> None:
 
 
 def customise_server(
-    server: lt.ThingServer, application_config: OFMApplicationData, debug: bool = False
+    server: lt.ThingServer, application_config: OFMApplicationData
 ) -> None:
     """Customise the server with additional endpoints, debug mode etc."""
     if DEVELOPER_MODE:
@@ -88,8 +88,9 @@ def customise_server(
     add_v2_endpoints(server)
     add_static_files(server, application_config.data_folder)
 
-    # Configure logging to DEBUG if requested in CLI args.
-    if debug:
+    # Configure logging to DEBUG if LT server is set up
+    # with debug = true
+    if server.debug:
         lt.logs.configure_thing_logger(logging.DEBUG)
 
     # Add an endpoint to get the logs - (directly calling the FastAPI decorator)
@@ -119,9 +120,8 @@ def serve_from_cli(argv: Optional[list[str]] = None) -> None:
         application_config = OFMApplicationData(**lt_config.application_config)
         configure_logging(application_config.log_folder)
 
-        server = lt.ThingServer.from_config(lt_config)
-        debug = bool(args.debug)
-        customise_server(server, application_config, debug)
+        server = lt.ThingServer.from_config(lt_config, args.debug)
+        customise_server(server, application_config)
 
         def shutdown_call() -> None:
             try:
diff --git a/tests/unit_tests/test_server_cli.py b/tests/unit_tests/test_server_cli.py
index 4c71a1c3..b7837781 100644
--- a/tests/unit_tests/test_server_cli.py
+++ b/tests/unit_tests/test_server_cli.py
@@ -109,14 +109,20 @@ def test_failed_customise(mocker):
     # An that it has the error to display
     assert str(fallback_app._context.error) == "Can't touch this"
 
-
 def test_debug_mode(mocker):
     """Test that --debug flag triggers lt.logs.configure_thing_logger."""
-    # Mock the LabThings function that returns the server
+
+    # Use a side_effect to map the CLI debug arg to the mock server's debug attribute
+    def mock_from_config(_, debug_flag):
+        mock_server = mocker.Mock()
+        mock_server.debug = debug_flag  # This will now be correctly True or False
+        return mock_server
+
     mocker.patch(
         "openflexure_microscope_server.server.lt.ThingServer.from_config",
-        return_value=mocker.Mock(),
+        side_effect=mock_from_config,
     )
+
     # Mock customisation dependencies to avoid side effects
     mocker.patch.object(ofm_server, "add_v2_endpoints")
     mocker.patch.object(ofm_server, "add_static_files")