Preheat oven to 350 degrees. In a large mixing bowl, add the almond flour, protein powder, cacao powder, coconut sugar, baking soda and salt. Whisk to combine.
In a smaller mixing bowl, add the eggs, applesauce, and milk. Whisk to combine.
Then pour the wet ingredients into the dry ingredients and use a wooden spoon to stir until the batter comes together. Next, add the chocolate chips and give it one more stir.
Spray an 8x8 inch baking dish with cooking spray, then pour the batter into the dish. Use the back of a spoon to smooth out the top.
Use a spoon to dollop the peanut butter all over the top of the batter, then use a butter knife to swirl the peanut butter all over the batter. There is no specific technique to this, just swirl it in all directions.
Bake for 30-35 minutes. Allow to cool for at least 10 minutes before cutting and serving.