Preheat oven to 350℉ and line an 8x8 baking pan with parchment paper.
Make the crumble topping. In a mixing bowl, stir together whole wheat pastry flour, brown sugar, apple pie spice, and salt. Add the room-temperature butter and stir with a fork or your hands until it forms a crumbly topping. Place in the fridge while you make the batter.
Make the batter. In a mixing bowl, whisk together the plain Greek yogurt, eggs, milk, maple syrup, applesauce, and vanilla extract until no lumps remain. Add the flour, protein powder, apple pie spice, baking powder, and baking soda and stir until well combined. Set aside.
Make the apple filling. Toss the chopped apples in a small bowl with 3 tbsp brown sugar and 1 tsp apple pie spice. Set aside.
Pour the batter into the prepared baking pan and smooth into an even layer. Top evenly with the apples, then sprinkle the chilled crumble topping over the apples. Bake in the preheated oven for 50-60 minutes, or until baked through.
Allow to cool in the pan for a few minutes, then transfer to a cooling rack to finish cooling. Slice into 9 squares and serve!