Cook for about 5 minutes until the peppers are tender. Move the mixture to one side of the pan and add in the spinach. Cover the pan with a lid to allow the spinach to wilt. This should only take a minute or two. Once the spinach is wilted, stir together with the cooked pepper mixture. Remove from heat and evenly distribute the vegetable mixture into the 12 slots of the muffin pan.
Bake in the preheated oven for about 15-20 minutes, until the egg muffins are firm to the touch.