Preheat oven to 350°F. Generously spray a 12-cup muffin tin with cooking spray.
In a large bowl, whisk together eggs, milk, salt, and pepper until well combined.
Divide crumbled bacon, bell peppers, onion, and ¾ cup cheese evenly among the muffin cups.
Pour egg mixture over the ingredients in each cup, filling about ¾ full. Top with remaining cheese.
Bake for 18-20 minutes until eggs are set and tops are lightly golden.
Let cool completely in the pan, then remove and store in an airtight container in the refrigerator for up to 3 days.
To reheat: Place on a baking sheet and warm in a 350°F oven for 8-10 minutes, or microwave individual cups for 30-45 seconds.