In a large mixing bowl or your stand mixer bowl, combine both flours, brown sugar, cocoa, salt, baking powder, and baking soda; mix well.
In a small mixing bowl, whisk the eggs, applesauce, milk, oil and vanilla. Slowly add this mixture to the dry ingredients until just moistened. Fold in the chocolate chips with a spatula or spoon.
Coat muffin pans with cooking spray OR place cupcake liners in the cups. Fill each cup 3/4 full with batter.
Bake at 350° for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Allow to cool for a few minutes before removing from the pans. Place on a wire rack after they cool for a bit. These are awesome served warm!