Preheat the oven to 350°F and coat the cups of a 12-slot muffin tin generously with non-stick spray.
In a blender, combine the eggs, cottage cheese, salt, and pepper, and blend until the mixture is fully emulsified and smooth.
Transfer the blended mixture to a mixing bowl and gently fold in the shredded Gruyère cheese.
Distribute the egg mixture evenly among the muffin tin cavities, filling each approximately two-thirds full to allow room for expansion during baking.
Sprinkle the chopped bacon over each portion, pressing lightly so the pieces settle into the egg mixture.
Bake for 20 to 25 minutes, or until the egg bites have set completely and the tops are slightly golden.
Once removed from the oven, allow the egg bites to rest in the pan for 5 to 10 minutes before using a spoon to carefully lift them out. Serve warm.