Preheat oven to 350 degrees F (175 degrees C). Spray an 8-inch baking dish with cooking spray.
Mix apple, banana, yogurt, almond butter, and eggs together in a bowl. Mix flour, chocolate chips, and protein powder together in a large bowl. Stir apple mixture into flour mixture until well combined; pour into the prepared baking dish.
Bake in the preheated oven until cooked through, 15 to 20 minutes.