Preheat your oven to 350 degrees.
Spray a cupcake pan with a non-stick spray.
Use a large bowl and add your eggs, milk, salt, and pepper. Stir to combine.
Begin to dice your onions into small bits.
Dice your tomatoes into quarters.
Roughly chop your spinach into halves.
Add your spinach, onions, and tomatoes.
Add all of your vegetables into your egg mix and stir to combine.
Pour out your egg mixture into the muffin pans equally into 12 parts.
Bake your egg muffins for 20 to 25 minutes.
Remove from the oven and let settle for 5 minutes.
Remove each muffin from the pan and top with garnishments.