Preheat oven to 350°F (175°C) and grease 6 cups of a standard muffin tin with cooking spray.
In a large mixing bowl, whisk the eggs until well combined and slightly frothy.
Season the eggs with salt and black pepper.
Fold in the chopped spinach, diced bell peppers, and diced onions.
Pour the egg mixture into the prepared muffin cups, filling each approximately 3/4 full.
Top each muffin with a portion of the shredded cheddar cheese.
Bake for 18 to 22 minutes, or until the eggs are firm to the touch and the tops have risen.
Allow the muffins to cool in the pan for 5 minutes before using a knife to loosen the edges and removing them.