Preheat oven to 350°F and grease a 12-cup muffin tin or line with paper liners.
Dice vegetables into small, 1/4-inch pieces. Use pre-cooked meat only.
Whisk eggs, milk, salt, and pepper together until fully blended.
Spoon vegetables and meat evenly into the bottom of each cup, then top with cheese.
Pour the egg mixture over the mix-ins, filling each cup about 3/4 full.
Bake for 18 to 20 minutes, until tops are set and a toothpick comes out clean.
Cool in the pan for 5 minutes on a wire rack.
Loosen edges with a knife, remove, and store in the fridge up to 4 days or freeze up to 2 months.