Preheat and prep: Heat your oven to 350°F (175°C).
Grease a 12-cup muffin tin generously with oil or butter, or use silicone cups for easy release.
Cook any raw add-ins: Sauté mushrooms, onions, or peppers until soft and most moisture has evaporated. Let them cool slightly. If using bacon or sausage, cook and drain well.
Whisk the base: In a large bowl, whisk eggs with milk or cream until smooth.
Season with 1/2 to 1 teaspoon salt and 1/4 to 1/2 teaspoon black pepper. Add a pinch of garlic powder or paprika if you like.
Add cheese and fillings: Stir in shredded cheese and your chosen add-ins. Aim for about 2 to 2 1/2 cups total fillings so the muffins are hearty but still hold together.
Fill the tin: Divide the mixture evenly among the muffin cups, filling each about 3/4 full.
Stir between pours to keep fillings evenly distributed.
Bake: Place on the center rack and bake 16–20 minutes, until the tops are set and a toothpick comes out clean or with just a few moist bits.
Rest and release: Let the muffins cool in the pan for 5 minutes. Run a thin knife around the edges, then lift out gently. Transfer to a wire rack to finish cooling.
Serve or store: Enjoy warm, or let cool completely for meal prep.
Add hot sauce, salsa, or a dollop of Greek yogurt if you like.