Preheat oven to 350.
Lightly grease 12 muffin cups. (You could also line with muffin liners, but if you're going to freeze any of them for later, I think it works better without the liners.)
Heat a large skillet and cook ground beef until crumbly. Drain grease (if any) and set aside.
Whisk eggs and milk in a large bowl.
Add onion, bell peppers, garlic, and salt and pepper
Evenly distribute the egg mixture into the muffin cups. Approximately 1/3 mixture cup into each muffin cup.
Sprinkle an even amount of cooked ground beef into each cup
Top each cup with cheese
Bake for approximately 20 minutes, or until eggs are set and a knife inserted at center comes out clean.