Prep the pan and oven: Preheat your oven to 350°F (175°C). Grease a 12-cup muffin tin generously with cooking spray or oil to prevent sticking.
Sauté the veggies: Warm a skillet over medium heat and add olive oil or butter. Cook the onion and bell pepper with a pinch of salt for 3–4 minutes, until slightly softened.
Stir in spinach and cook 1–2 minutes more, just until wilted. Remove from heat and let cool slightly.
Mix the eggs: In a large bowl, whisk eggs, milk, garlic powder, smoked paprika, salt, and pepper until smooth and lightly frothy. Stir in the herbs.
Layer the add-ins: Divide the sautéed veggies evenly among the muffin cups.
If using cherry tomatoes, add a few pieces to each cup. Sprinkle cheese over the top of the vegetables.
Pour in the egg mixture: Carefully pour the egg mixture into each cup, filling about 3/4 full. Give the tin a gentle tap on the counter to release air bubbles and level the tops.
Bake: Place the tin on the middle rack and bake for 16–20 minutes, or until the muffins are set in the center and lightly golden around the edges.
They may puff up, then settle as they cool.
Cool and release: Let the muffins cool in the pan for 5 minutes. Run a thin spatula or butter knife around the edges to loosen, then lift out carefully.
Serve or store: Enjoy warm, or let them cool completely for meal prep. Add hot sauce, salsa, or a dollop of yogurt if you like.