Grease your muffin tins and set them aside. Beat eggs in a medium-sized bowl, add salt and black pepper. Whisk to combine.
Fold in chopped cherry tomatoes, basil leaves, and shredded cheese. Stir to combine. Divide the egg mixture into 16 to 18 muffin molds evenly filling about 3/4 of the way full.
Bake for 20-25 minutes until the egg muffins are set in the middle and begin to turn golden brown. Remove from the oven and let cool before removing from the muffin tin.