Preheat the oven to 375°F. Line a 12-cup muffin tin with paper or silicone liners and set aside.
Peel the bananas and add them to a large mixing bowl. Mash thoroughly with a fork until smooth with no large lumps remaining. The riper the bananas the easier this step will be and the sweeter the finished muffins will taste.
Add the coconut sugar, egg, and unsweetened applesauce to the mashed banana. Stir until fully combined.
In a separate bowl whisk together the wheat flour, unsweetened cocoa powder, salt, baking soda, and baking powder until evenly combined.
Add the dry ingredients to the wet ingredients and stir gently until just combined. Do not overmix. A few small lumps are fine and overmixing will make the muffins dense rather than tender.
Fold in the dark chocolate chips until evenly distributed throughout the batter.
Divide the batter evenly among the 12 lined muffin cups filling each one about two thirds full.
Bake for 18 to 20 minutes until a toothpick inserted into the center of a muffin comes out with just a few moist crumbs. The tops should look set and the edges will just begin to pull away from the liners.
Allow to cool in the pan for 5 minutes then transfer to a wire rack to cool for another 5 minutes before serving.