Preheat oven to 325°F. Line muffin pan with 12 muffin liners or spray with cooking spray.
Mix flours, sugar, baking powder, and salt in a large bowl.
In a medium bowl, mash banana and mix with egg, honey, applesauce, and milk. Stir banana mixture into dry ingredients until just blended (do not over-mix). Fold in chocolate chips.
Divide batter equally among prepared muffin cups, filling each about 3/4 full. Bake for 35-40 minutes or until tops are pale golden and toothpick inserted into center comes out clean. Transfer muffins to rack and cool before serving.