Preheat the oven to 350 degrees F (175 degrees C). Spray 2 mini muffin tins with nonstick cooking spray. Heat a medium-sized skillet over medium heat and spray with cooking spray. Add onion and cook gently, 1 to 3 minutes. Add spinach and cook until wilted, about 1 minute more. Remove from heat and allow to cool slightly. Whisk egg whites and egg together in a bowl. Add Cheddar cheese and season with black pepper. Stir cooled spinach mixture into eggs. Spoon mixture into each mini muffin cup, filling them halfway. Bake in the preheated oven until set and puffed up, about 15 minutes.