Preheat: Preheat oven to 350°F (177°C).
Cook veggies: Melt butter in a skillet over medium high heat. Add onion, cook until softened, about 3 minutes. Add mushrooms and red pepper. Cook until onion is golden brown and mushrooms are softened, about 5 minutes. Stir in spinach, cook until it begins to wilt, about 1 minute. Remove from heat.
Whisk eggs: Meanwhile, in a large bowl, whisk together eggs, milk, pesto, salt and pepper.
Assemble: Lightly spray a muffin pan or line with paper muffin cups (see note 1). Divide veggies into the cups, then sprinkle with feta. Pour egg mixture on top.
Bake: Bake until the eggs are set in the middle, about 18 minutes. Let cool slightly, then lift from pan. Cover and refrigerate extras (see note 2).
