In a large mixing bowl, whisk the eggs and the cottage cheese until well combined.
Fold in the bacon and the shredded cheese, then add salt and pepper to taste.
Spoon the mixture into a 24-count silicone muffin tin until 3/4 full.
Add about an inch of water to a 9x13-inch baking dish. Place the silicone muffin tin inside the baking dish so the eggs can cook slowly in a water bath.
Cook the egg bites for 25-30 minutes, until the eggs are cooked through.
Notes
If you do not have a 9x13-inch baking pan that the muffin tin will set inside, you can fill a casserole dish with an inch of water and place it on the bottom rack of the oven. Then cook the egg bites on the middle or top rack.
You can blend the eggs and cottage cheese in a blender until smooth if you dislike the texture of cottage cheese curds.
Store in an airtight container in the fridge for 4 days, or in the freezer for 3 months. Reheat in a 350F oven for 5-10 minutes, or in a microwave on 80% power in 20-second increments.