Heat the oven to 350°F (180°C). Grease a 12-cup muffin tin or line it with silicone liners.
Add the eggs, cottage cheese, salt, and pepper to a blender. Blend for about 30 seconds, until completely smooth with no visible curds.
Divide your mix-ins between the muffin cups. Keep the pieces small so they spread evenly.
Pour the egg mixture over the mix-ins, filling each cup about three quarters full.
Bake for 17 to 19 minutes, until the egg bites are set in the center and lightly golden on top.
Let them cool in the tin for a few minutes, then lift them out. Serve warm or store for later.