Preheat oven to 350°F (175°C). Generously grease a 12-cup muffin tin or use silicone liners.
In a mixing bowl, whisk together eggs, milk, salt, and pepper until smooth. Let the mixture rest for 2–3 minutes to reduce air bubbles.
Divide chopped vegetables, cheese, and any optional meat evenly among muffin cups.
Pour the egg mixture over the fillings, filling each cup about ¾ full. Gently stir each one with a fork.
Optional: Place the muffin tin into a larger baking dish and fill the outer dish with hot water for a water bath.
Bake for 18–22 minutes, or until the centers are set and tops are lightly golden. Let cool in the pan for 5 minutes, then remove.
Serve immediately or cool completely and store in the fridge or freezer for later use.