Position one oven rack to the very bottom position and another to the middle position. Preheat the oven to 300°F. Grease a 12-count muffin tin with cooking spray. Fill a 9x12-inch baking pan with 2 inches of very hot water and carefully place in the lowest position in the oven. This creates steam for even cooking and a custardy texture.
Add the eggs, cottage cheese, shredded cheese, salt, and pepper to a blender. Blend until smooth.
9 large eggs, 1 1/2 cups cottage cheese, 1/2 cup shredded cheddar cheese, 1 teaspoon kosher salt, 1/2 teaspoon black pepper
Heat the olive oil in a nonstick skillet over medium heat. Add the bell pepper and cook until soft, 2-3 minutes and transfer to a medium bowl. Add the spinach and cook to wilt. Remove to a paper towel and pat out the excess water. Place it in the bowl with the cooked peppers and the scallions.
2 teaspoons olive oil, 1 red bell pepper, 2 cups spinach, 1/4 cup chopped green onion
Divide the veggie mixture between the prepared muffin tins, reserving about 1/4 cup for the tops. Pour the egg mixture over the veggies until the muffin tins are 3/4 of the way full. Top with the reserved veggies.
Place the egg bites on the middle rack and bake for 30-35 minutes, until the tops are puffed up and set. They will deflate slightly as they cool. Let them cool in the pan for 10 minutes then run a knife around the edge and pop them out.