Preheat the oven to 350F and grease a 24-count mini muffin pan; if using a regular 12-count muffin pan, increase baking time as noted.
In a large bowl whisk 6 eggs and 3 tablespoons milk until combined, then stir in 1 cup chopped pizza toppings and 1 cup shredded mozzarella.
Divide the egg mixture evenly among the muffin cups, filling each about 3/4 of the way up.
Bake in the preheated oven for 15-18 minutes. Remove the pan from the oven and let the egg cups cool in the pan before carefully loosening them with a small knife or small spatula.
Once cooled, refrigerate the egg cups in an airtight container or zip bag for up to 3 days.
For room-temperature snacks, place 4 to 6 egg cups in the main compartment of a lunch container.
To serve warm, heat the egg cups in the microwave for 1 minute, stopping halfway to flip them, then transfer immediately into a thermos and close the lid.
Finish packing the snack box by adding fruit, veggies, and any other sides into a bento or lunch bag.