Preheat the oven to 300 degrees F. Arrange an oven rack in the center spot. Place the silicone liners into the muffin tin cups. Set aside.
Add the eggs, cottage cheese, and Gruyere to a blender. Cover and blend for 20-30 seconds.
Pour 1/4 cup of the mixture into each muffin liner. (If there are some cheese remnants at the bottom of the blender, just distribute them between the cups or discard them.) Add 2 teaspoons of bacon to each cup.
Bake for 28-30 minutes or until the egg is set (not jiggly) in the center.
Remove from the oven and let rest for 5 minutes in the pan. Then, carefully release the egg bites from the liners onto a wire rack to cool or enjoy them warm.
Notes
You can use paper liners instead of silicone liners. Just be sure to grease paper liners generously with non-stick cooking spray.