Preheat oven to 400 degrees F.
Line muffin tins with cupcake liners or spray with nonstick cooking spray.
In a large mixing bowl, combine cocoa powder, protein powder, whole wheat flour, Truvia, baking powder and baking soda.
Mix in eggs, milk, applesauce, vanilla and vegetable oil until well combined.
Fill each cupcake liner 2/3 of the way full or use a large cookie scoop to place batter in cups.
Sprinkle a few chocolate chips on top of each muffin before baking.
Bake for 20 minutes or until set in the center.