Preheat oven to 350°F. Spray muffin tins (18 wells) with nonstick cooking spray with flour. Set aside.
In a shallow bowl, mash bananas and set aside.
In a medium bowl, whisk together flour, cocoa powder, baking soda, baking powder, and salt. Stir in mini chocolate chips. Set aside.
In a larger bowl add sugar, applesauce, oil, vanilla extract, and eggs. Add mashed bananas and whisk to combine ingredients. Stir in flour mixture until just combined, without over mixing. Spoon batter evenly into prepared muffin tins.
Sprinkle each muffin with mini chocolate chips gently pressing them into the batter.
Bake for 20 - 23 minutes or until a toothpick inserted in the center of a muffin comes out clean. Cool muffin tins on a wire rack for 10 minutes. Remove muffins from tin to cool. Enjoy warm or at room temperature.