Preheat oven to 350 degrees F (175 degrees C). Line 12 muffin cups with paper liners.
Mix bananas, egg, coconut sugar, almond butter, cocoa powder, vanilla extract, baking soda, cinnamon, and sea salt together in a bowl using an electric mixer; add almond flour and tapioca flour and mix well. Fold chocolate chips into batter and spoon into the prepared muffin cups.
Bake in the preheated oven until a toothpick inserted in the center comes out clean, about 20 minutes.
