Preheat your oven to 375°F (190°C). Grease a 12-cup muffin tin with cooking spray or line it with silicone muffin liners for easy removal.
In a large mixing bowl, whisk together the eggs, milk, salt, and pepper until fully combined and slightly frothy.
Stir in your desired mix-ins, such as shredded cheese, cooked meat, chopped veggies, or fresh herbs. Mix gently to distribute evenly.
Divide the egg mixture evenly among the 12 muffin cups, filling each about ¾ full to allow room for the egg cups to rise.
Bake in the preheated oven for 15–20 minutes, or until the egg cups are puffed, golden, and set in the center. To check doneness, insert a toothpick into the center—it should come out clean.
Let the egg cups cool in the pan for 5 minutes before carefully removing them. Serve warm or let them cool completely before storing.
