Preheat the oven to 375°F and position a rack in the center. Line a muffin tin with baking cups and set it aside.
In a large bowl mash the bananas with a fork or potato masher then mix in the sugar, egg, applesauce, and peanut butter until combined. Stir in the flours, cocoa powder, salt, baking soda, and baking powder over the banana mixture. Mix lightly with a rubber spatula to combine. Fold in chocolate chips. The batter should be just moistened but still a little clumpy. Don’t overmix!
Using a spring-loaded ice cream scoop or spoons, divide the batter between the prepared muffin cups and bake them for about 20 minutes until a toothpick inserted into the middle comes out clean. Transfer them to a rack to cool. Store muffins in an airtight container at room temperature for up to 3 days.