Preheat and prep: Heat the oven to 350°F (175°C).
Lightly grease a 12-cup muffin tin with cooking spray or oil. This helps prevent sticking.
Sauté the veggies: Warm the oil or butter in a skillet over medium heat. Add onion and bell pepper; cook 3–4 minutes until softened.
Stir in garlic and chopped spinach; cook 1–2 minutes until the spinach wilts. Remove from heat and cool slightly.
Whisk the eggs: In a large bowl, whisk the eggs with milk, salt, pepper, and smoked paprika or chili flakes if using. Whisk until the mixture looks uniform and slightly frothy.
Add cheese and herbs: Stir in the shredded cheese, Parmesan, and fresh herbs.
Fold in the cooled veggie mixture.
Fill the tin: Divide the egg mixture evenly among the muffin cups. Aim to fill each cup about 3/4 full to allow room for puffing.
Bake: Place the tin on the middle rack and bake for 16–20 minutes, or until the centers are just set and the edges are lightly golden. A toothpick should come out mostly clean.
Cool and release: Let the muffins rest in the pan for 3–5 minutes, then run a thin knife around the edges to loosen.
Transfer to a cooling rack.
Serve: Enjoy warm, or let them cool completely for storage. They pair well with hot sauce, salsa, or a side of fruit.