Preheat oven to 375F. Spray a muffin pan with cooking spray.
Place broccoli in a bowl and microwave covered until tender, about 1-2 minutes.
Whisk eggs, cottage cheese, salt, and pepper in a bowl. Add broccoli and stir to combine.
Pour egg mixture into muffin cups and top with cheddar and parmesan. Bake until top is browned and center is set, about 20-30 minutes.
