Preheat oven to 350°F (175°C). Grease a 12-cup muffin tin with nonstick spray.
In a large bowl, whisk eggs, milk, salt, pepper, and everything bagel seasoning (if using cream cheese option).
Pour half of the egg mixture evenly into muffin cups.
Add your preferred fillings (except grated cheese).
Pour remaining egg mixture on top.
Sprinkle cheese if using.
Bake Customizable Egg Muffins for 20–25 minutes until set and lightly golden.
Let cool slightly before serving.