Preheat and prep: Heat the oven to 350°F (175°C). Spray a 12-cup muffin pan generously with nonstick spray or line with silicone or parchment liners.
Sauté the veggies: Warm the olive oil or butter in a skillet over medium heat.
Add onion and mushrooms, cook 3–4 minutes until softened. Stir in bell pepper and a pinch of salt; cook 2–3 minutes more. Add spinach and cook just until wilted.
Remove from heat and let cool slightly.
Whisk the eggs: In a large bowl, whisk eggs, milk, salt, pepper, garlic powder, and red pepper flakes until well combined and slightly frothy. Froth helps the muffins rise and stay light.
Add mix-ins: Fold in the sautéed veggies, herbs, and most of the cheese. Reserve a little cheese to sprinkle on top.
Fill the pan: Divide the mixture evenly among the muffin cups, filling about 3/4 full.
Top with the remaining cheese and a little chopped tomato, if using.
Bake: Bake for 16–20 minutes, or until the centers are set and a toothpick comes out mostly clean. They will puff while baking and settle as they cool.
Cool and release: Let the muffins cool in the pan for 5 minutes, then run a thin knife around the edges to loosen and lift out. This helps prevent tearing.
Serve: Enjoy warm, or cool completely for meal prep.