Preheat oven to 350 degrees Fahrenheit (175 degrees Celsius) and grease a 12-cup muffin tin thoroughly.
In a large mixing bowl, whisk together eggs, milk, salt, and pepper until the mixture is uniform.
Divide the chopped spinach and diced red bell pepper evenly across the 12 muffin cups.
Pour the egg mixture into each cup until it reaches approximately 3/4 of the way to the top.
Top each cup with a portion of the shredded cheddar cheese.
Bake for 20 to 22 minutes until the eggs are puffed, set in the center, and lightly golden.
Allow the muffins to cool in the pan for 5 minutes to allow for easier release before serving.