Preheat the oven to 300°F (150°C). Place a 12-cup silicone muffin pan onto a rimmed baking sheet.
Place a separate roasting pan filled with 1 inch of hot water on the bottom rack of the oven to create a humid environment.
Add the eggs, cottage cheese, egg whites, salt, and pepper into a high-speed blender.
Emulsify the mixture on medium-high speed for 30 to 45 seconds until completely smooth and slightly frothy.
Distribute the chopped spinach and crumbled bacon evenly across the bottom of the 12 muffin cups.
Divide the egg mixture evenly among the cups, filling each to approximately 80% capacity.
Sprinkle the shredded cheddar cheese over the top of each cup.
Bake for 30 minutes or until the egg bites are set and the internal temperature reaches 165°F (74°C).
Remove from the oven and allow the bites to rest in the silicone mold for 5 minutes to facilitate clean release.
Carefully depan the egg bites and serve immediately or refrigerate for meal prep.