Preheat oven to 300°F (150°C) and place a 9x13 inch baking dish filled with 1 inch of hot water on the bottom rack to create a steam environment.
In a high-speed blender, combine the eggs, cottage cheese, shredded cheddar cheese, salt, and pepper.
Process on high speed for 30 to 45 seconds until the mixture is completely smooth and aerated.
Lightly coat a 12-cup silicone muffin pan with non-stick cooking spray.
Distribute the bacon bits and chives evenly into the bottom of each muffin cup.
Pour the blended egg mixture into each cup, filling them approximately 7/8 of the way to the top.
Place the silicone tray on a metal baking sheet for stability and place it on the center rack of the oven.
Bake for 25 to 30 minutes until the egg bites are set and the tops are slightly firm to the touch.
Remove from the oven and allow to rest in the pan for 5 minutes before gently popping them out of the silicone mold.