diff --git a/src/CSET/__init__.py b/src/CSET/__init__.py
index 0df82db82..dda73b5d8 100644
--- a/src/CSET/__init__.py
+++ b/src/CSET/__init__.py
@@ -88,15 +88,23 @@ def main():
         default=None,
     )
     parser_cookbook.set_defaults(func=_cookbook_command)
-
     args = parser.parse_args()
 
-    # Logging verbosity
+    # Setup logging.
     if args.verbose >= 2:
-        logging.basicConfig(level=logging.DEBUG)
-    elif args.verbose >= 1:
-        logging.basicConfig(level=logging.INFO)
-
+        loglevel = logging.DEBUG
+    elif args.verbose == 1:
+        loglevel = logging.INFO
+    else:
+        loglevel = logging.WARNING
+    logger = logging.getLogger()
+    logger.setLevel(min(loglevel, logging.INFO))
+    stderr_log = logging.StreamHandler()
+    stderr_log.addFilter(lambda record: record.levelno >= loglevel)
+    stderr_log.setFormatter(logging.Formatter("%(asctime)s %(levelname)s %(message)s"))
+    logger.addHandler(stderr_log)
+
+    # Execute the specified subcommand.
     if args.subparser:
         args.func(args)
     else:
diff --git a/src/CSET/operators/__init__.py b/src/CSET/operators/__init__.py
index 5a5637410..7f6e11d9a 100644
--- a/src/CSET/operators/__init__.py
+++ b/src/CSET/operators/__init__.py
@@ -154,9 +154,18 @@ def step_parser(step: dict, step_input: any) -> str:
 
     original_working_directory = Path.cwd()
     os.chdir(output_directory)
-    # Create metadata file used by some steps.
-    _write_metadata(recipe)
     try:
+        logger = logging.getLogger()
+        diagnostic_log = logging.FileHandler(
+            filename="CSET.log", mode="w", encoding="UTF-8"
+        )
+        diagnostic_log.addFilter(lambda record: record.levelno >= logging.INFO)
+        diagnostic_log.setFormatter(
+            logging.Formatter("%(asctime)s %(levelname)s %(message)s")
+        )
+        logger.addHandler(diagnostic_log)
+        # Create metadata file used by some steps.
+        _write_metadata(recipe)
         # Execute the recipe.
         for step in recipe["steps"]:
             step_input = step_parser(step, step_input)