Preheat oven to 325 degrees. Add water 3/4 the way up a 9x13 casserole dish and place on the bottom oven rack to warm while preparing the other ingredients.
To a blender, add eggs, cottage cheese, salt and pepper. Pulse 5-10 times until eggs and cottage cheese are combined and homogenous- do not blend and make mixture frothy.
Transfer silicone muffin pan atop a sheet pan and evenly disperse add-ins to the bottoms of each cup. Pour the egg mixture evenly atop each cup.
Transfer the pan to the middle or top rack of the oven, above the simmering water. The water will release steam keeping the egg bites fluffy and moist.
Bake for 20-25 minutes, rotating the pan 180 degrees halfway through cooking, until egg bites are set and popping out of the cups.
Serve immediately or chill completely and store in pyrex to warm for breakfasts. Egg bites will stay fresh throughout the work week kept in a well-sealed container in the fridge.