First, preheat the oven to 350° F. Spray 6 cups in a muffin tin generously with nonstick spray.
In a large bowl, whisk the eggs, followed by cheese, cottage cheese, salt, and pepper.
Pour six equal amounts of the mixture into the muffin tins. Top with bacon bits.
Bake doe 30 minutes, or until the eggs are completely cooked. Remove from the oven, take out of the tin, and serve the egg bites warm.