diff --git a/lib/config.js b/lib/config.js
index 7b8ac77a..41ff4bf5 100644
--- a/lib/config.js
+++ b/lib/config.js
@@ -15,8 +15,8 @@ class Config {
             verbose: args.verbose,
             // Command specific options
             lint: {
-                rules: args.rules,
-                skip: args.skip,
+                rules: this.notEmptyArray(args.rules),
+                skip: this.notEmptyArray(args.skip),
             },
             resolve: {
                 output: args.output,
@@ -71,6 +71,17 @@ class Config {
         });
         return cleaned;
     }
+
+    /**
+     * Check and returns the given array if it is not empty. Otherwise it returns 'undefined'.
+     * Useful for configuration options where an empty array has no meaning.
+     *
+     * @param array The array instance to check.
+     * @returns {array|undefined} The given array; or 'undefined' if array is 'undefined' or empty.
+     */
+    notEmptyArray(array) {
+        return array && array.length > 0 ? array : undefined;
+    }
 }
 
 module.exports = new Config;
diff --git a/lint.js b/lint.js
index e49ad1d8..d1424cc0 100644
--- a/lint.js
+++ b/lint.js
@@ -69,8 +69,8 @@ const command = async (specFile, cmd) => {
     config.init(cmd);
     const jsonSchema = config.get('jsonSchema');
     const verbose = config.get('quiet') ? 0 : config.get('verbose', 1);
-    const rulesets = config.get('lint:rules');
-    const skip = config.get('lint:skip');
+    const rulesets = config.get('lint:rules', []);
+    const skip = config.get('lint:skip', []);
 
     rules.init({
         skip
diff --git a/test/lib/config.test.js b/test/lib/config.test.js
index 1b03cacd..11a6832a 100644
--- a/test/lib/config.test.js
+++ b/test/lib/config.test.js
@@ -38,6 +38,20 @@ describe('Config', () => {
                     'https://example.org/my-rules.json',
                 ]);
             });
+
+            test('meaningless empty arrays in default config must not override options of config file', () => {
+                config.init({ config: configFile, rules: [], skip: []});
+
+                expect(config.get('lint:rules')).toEqual([
+                    'strict',
+                    './some/local/rules.json',
+                    'https://example.org/my-rules.json',
+                ]);
+
+                expect(config.get('lint:skip')).toEqual([
+                    'info-contact',
+                ]);
+            });
         });
     });