Preheat your oven to 350°F and coat a 12-cup muffin tin thoroughly with non-stick cooking spray. Blend together the eggs, cottage cheese, salt, and pepper until the mixture is completely smooth. Transfer the blend to a bowl and gently fold in the shredded Gruyere cheese. Pour the egg mixture evenly into the prepared muffin cups, ensuring each is filled about two-thirds full to allow room for the eggs to puff up as they bake. Sprinkle the chopped bacon over each cup and lightly press it down with a spoon so it is submerged in the egg mixture. Bake for 20 to 25 minutes or until the egg bites are fully set. Remove from the oven and allow them to rest for 5 to 10 minutes before carefully loosening each bite with a spoon. Serve warm and savor immediately.