Preheat the oven to 350 degrees F (175 degrees C). Spray 12 muffin cups with cooking spray.

Heat olive oil in a skillet over medium heat. Add asparagus, green bell pepper, and onion; cook and stir until vegetables are softened.

Whisk eggs, milk, salt, and black pepper together in a bowl. Stir cooked vegetables and Cheddar cheese into the egg mixture.

Spoon about 1/4 cup of mixture into each muffin cup.