Preheat the oven to 425 degrees F, and lightly grease a 12-cup muffin pan with baking spray.
In a medium bowl, whisk together the whole wheat flour, all-purpose flour, cocoa powder, salt, baking powder and baking soda. In a separate large bow, whisk together the applesauce, sugar, honey, egg whites, yogurt, and vanilla until smooth. Slowly stir the wet ingredients into the dry, taking care not to over-mix. Stir in the chocolate chips.
Divide the batter evenly into the prepared pan, filling all the way to the top, and sprinkle a few extra chocolate chips on top of each muffin.
Bake for 5 minutes, then reduce the oven temperature to 375 degrees F and bake for an additional 13 minutes, or until a toothpick inserted in the center comes out clean.