Preheat oven to 350°F (175°C) and grease a 12-cup muffin pan with nonstick spray.
In a large bowl, whisk together eggs, milk, salt, pepper, and everything bagel seasoning (if using cream cheese variation).
Pour half of the egg mixture evenly into muffin cups.
Add your desired fillings (except grated cheese).
Pour the remaining egg mixture on top.
Sprinkle grated cheese over each muffin if using.
Bake for 20–25 minutes until the egg muffins are puffed and set.
Let cool slightly before removing from the pan.
These Customizable Egg Muffins can be mixed and matched to suit your taste preferences.