Preheat oven to 350 degrees F. Line a 12-cup muffin pan with muffin liners or grease with cooking spray.
In a large bowl, stir together the flours, cocoa, baking powder, baking soda, and salt.
In a separate bowl, mix together the mashed banana, sugar, coconut oil, flax egg, and vanilla.
Pour the wet ingredients into the bowl with the dry ingredients and stir just until combined, then stir in the chocolate chips (don't over-mix!).
Divide the batter evenly among the prepared muffin cups, and bake 20-22 minutes, until a toothpick inserted in the center comes out clean. Allow muffins to cool in the pan on a wire rack for at least 5 minutes, then remove and enjoy!