Preheat oven to 400 degrees. Spray 9 muffin tins with cooking spray.
Spray a medium saute pan with cooking spray, and saute onions and peppers until just tender, about 2-4 minutes. Set aside and let cool.
In a medium bowl, mix together eggs, cheese, salt and pepper and bell peppers/onions.
Divide egg mixture evenly between 9 muffin tins, and top each egg muffin with a tomato slice.
Bake 25-30 minutes, or until the eggs are set and cooked through, (no longer runny). Let cool slightly and remove muffins. Enjoy immediately, or store in the fridge for up to 7 days!