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 nonstick spray. Fill a 9×12-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.
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.
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.