Preheat oven to 325°F. Line muffin pan with cupcake liners.
Mix flours, sugar, baking powder, and salt in a mixing bowl. In a separate large bowl, mash up bananas, adding egg, honey, applesauce, and milk; mix well.
Add dry ingredients to the wet and stir until just blended; avoid over-mixing. Fold in chocolate chips (optional).
Fill each muffin cup ¾ full and bake for 30-35 minutes or until an inserted toothpick comes out clean.
Transfer to a cooling rack and allow to cool for 5 minutes before serving.