Preheat oven to 350°F. Coat a muffin pan generously with cooking spray.
Whisk together eggs and milk in a large bowl. Stir in cheese, ham, bell pepper, and onion. Pour mixture evenly into prepared pan.
Bake for 25 to 28 minutes or until muffins are set in the center. Let cool in pan for 15 minutes. Remove to a wire rack and cool completely.
Refrigerate leftover muffins up to 5 days. Reheat in the microwave 30 seconds or just until warm. You can also wrap completely cooled muffins individually in plastic wrap, and freeze in a zip-top plastic freezer bag up to 3 months.