diff --git a/cchecker.py b/cchecker.py
index 4e5ed5d4..1327a3b2 100755
--- a/cchecker.py
+++ b/cchecker.py
@@ -22,21 +22,25 @@ def _print_checker_name_header(checker_str):
 
 def parse_options(opts):
     """
-    Helper function to parse possible options.  Splits option after the first
-    colon to split into key/value pairs.
+    Helper function to parse possible options. Splits option into key/value
+    pairs and optionally a value for the checker option. The separator
+    is a colon.
 
     :param opts: Iterable of strings with options
     :rtype: dict
-    :return: Dictionary with keys as checker type (i.e. "cf", "acdd")
+    :return: Dictionary with keys as checker type (i.e. "cf", "acdd").
+             Each value is a dictionary where keys are checker options and values
+             are checker option values or None if not provided.
     """
-    options_dict = defaultdict(set)
+    options_dict = defaultdict(dict)
     for opt_str in opts:
         try:
-            checker_type, checker_opt = opt_str.split(":", 1)
+            checker_type, checker_opt, *checker_val = opt_str.split(":", 2)
+            checker_val = checker_val[0] if checker_val else None
         except ValueError:
             warnings.warn(f"Could not split option {opt_str}, ignoring", stacklevel=2)
         else:
-            options_dict[checker_type].add(checker_opt)
+            options_dict[checker_type][checker_opt] = checker_val
     return options_dict
 
 
@@ -174,8 +178,9 @@ def main():
                                     checkers.  Multiple options can be specified
                                     via multiple invocations of this switch.
                                     Options should be prefixed with a the
-                                    checker name followed by the option, e.g.
-                                    '<checker>:<option_name>'
+                                    checker name followed by the option,
+                                    potentially followed by a value, e.g.
+                                    '<checker>:<option_name>[:<option_value>]'
 
                                     Available options:
                                     'cf:enable_appendix_a_checks' - Allow check
@@ -235,7 +240,7 @@ def main():
         print(f"IOOS compliance checker version {__version__}")
         sys.exit(0)
 
-    options_dict = parse_options(args.option) if args.option else defaultdict(set)
+    options_dict = parse_options(args.option) if args.option else defaultdict(dict)
 
     if args.describe_checks:
         error_stat = 0
diff --git a/compliance_checker/base.py b/compliance_checker/base.py
index 4cf5e751..0f276754 100644
--- a/compliance_checker/base.py
+++ b/compliance_checker/base.py
@@ -157,7 +157,7 @@ def setup(self, ds):
     def __init__(self, options=None):
         self._defined_results = defaultdict(lambda: defaultdict(dict))
         if options is None:
-            self.options = set()
+            self.options = {}
         else:
             self.options = options
 
diff --git a/compliance_checker/suite.py b/compliance_checker/suite.py
index a548aae7..6b534f5f 100644
--- a/compliance_checker/suite.py
+++ b/compliance_checker/suite.py
@@ -401,7 +401,7 @@ def run_all(self, ds, checker_names, include_checks=None, skip_checks=None):
             #       use some kind of checker object with checker type and
             #       version baked in
             checker_type_name = checker_name.split(":")[0]
-            checker_opts = self.options.get(checker_type_name, set())
+            checker_opts = self.options.get(checker_type_name, {})
 
             # instantiate a Checker object
             try:
diff --git a/compliance_checker/tests/test_cf.py b/compliance_checker/tests/test_cf.py
index 3db25d2d..04ca15b2 100644
--- a/compliance_checker/tests/test_cf.py
+++ b/compliance_checker/tests/test_cf.py
@@ -240,7 +240,7 @@ def test_appendix_a(self):
         dataset = self.load_dataset(STATIC_FILES["bad_data_type"])
         # Ordinarily, options would be specified in the checker constructor, but
         # we set them manually here so we don't have to monkey patch `setUp`
-        self.cf.options = {"enable_appendix_a_checks"}
+        self.cf.options = {"enable_appendix_a_checks": None}
         new_check = copy.deepcopy(self.cf)
         self.cf.setup(dataset)
         aa_results = self.cf.check_appendix_a(dataset)
diff --git a/compliance_checker/tests/test_cli.py b/compliance_checker/tests/test_cli.py
index 2788ec25..670e5b27 100644
--- a/compliance_checker/tests/test_cli.py
+++ b/compliance_checker/tests/test_cli.py
@@ -7,9 +7,12 @@
 import json
 import os
 import platform
+import shutil
 import subprocess
 import sys
 from argparse import Namespace
+from collections import defaultdict
+from importlib.machinery import SourceFileLoader
 
 import pytest
 
@@ -268,3 +271,23 @@ def test_nczarr_pass_through(self, zarr_url):
             output_format="text",
         )
         assert not errors
+
+
+def test_parse_options():
+    """Test the option parser of cchecker.py"""
+    # Load cchecker.py
+    cchecker = SourceFileLoader("cchecker", shutil.which("cchecker.py")).load_module()
+    # Simple test checker_type:checker_opt
+    opt_dict = cchecker.parse_options(["cf:enable_appendix_a_checks"])
+    assert opt_dict == defaultdict(dict, {"cf": {"enable_appendix_a_checks": None}})
+    # Test case checker_type:checker_opt:checker_val
+    opt_dict = cchecker.parse_options(
+        ["type:opt:val", "type:opt2:val:2", "cf:enable_appendix_a_checks"],
+    )
+    assert opt_dict == defaultdict(
+        dict,
+        {
+            "type": {"opt": "val", "opt2": "val:2"},
+            "cf": {"enable_appendix_a_checks": None},
+        },
+    )