Preheat oven to 350 degrees F. Grease a standard 12 cup muffin tin with non-stick cooking spray.
In a large bowl, combine the dry ingredients: flours, sugar, cocoa, baking soda, cinnamon, salt and chocolate chips and stir to combine.
In a medium bowl, beat together the eggs, yogurt, milk, applesauce and vanilla. Make a well in the center of the dry ingredients and stir in the wet mixture, stirring just until moistened (don't over-mix).
Divide batter between muffin cups. Bake for 12-15 minutes or until a toothpick inserted in the center comes out clean. Remove to a wire rack to cool completely.
Freezing Instructions: Allow muffins to cool completely. Store them in a freezer-safe ziplock bag or air-tight container.