Preheat the oven to 350℉. Grease 9 muffin cups in a muffin pan by spraying with nonstick cooking spray. Set aside.
In a blender, add the eggs and cottage cheese, and run at high speed until it's completely smooth and blended well. This mixture will be the base for the egg bites, so you want whip and blend a lot of air into it, to create a fluffy texture.
6 large eggs, 1/2 cup cottage cheese
Add in the shredded gruyere cheese, chopped cooked bacon, kosher salt, and black pepper. Blend on low speed just until combined; you don't want to chop the bacon up into all finely ground pieces, leave larger chunks.
1/2 cup shredded Gruyere cheese, 4 strips cooked bacon, ¼ teaspoon kosher salt, ⅛ teaspoon black pepper
Evenly distribute the egg mixture into the greased muffin cups - filling each one about two-thirds full, to allow room for the egg bites to puff up during baking. Spoon out any remaining bacon or cheese from the blender and add it to the egg bites.
Place the muffin pan on a rimmed cookie sheet. Carefully fill the cookie sheet halfway full with water, ensuring you do not get any water in the egg bites or muffin pan.
Cook for 20-25 minutes or until the egg bites are set and the tops are slightly golden brown.
When done, remove the pan from the oven and let the egg bites cool in the warm muffin pan. Use a knife to gently loosen the sides of the egg bites from the muffin cups, then remove them and serve warm.