Preheat oven to 375 degrees F (180 degrees C). Grease a 12-muffin pan with cooking spray.
In a large bowl, mix the mashed bananas, oil, applesauce, eggs, sugar, and vanilla together.
In another bowl, mix together the all-purpose flour, cinnamon, baking powder, baking soda, and salt. Mix the dry ingredients with the wet ingredients.
In a microwave-safe bowl, heat the chocolate chips for a minute and check them. Continue microwaving the chips in 20-second increments until all the chips have a glossy sheen. Stir the chocolate together until you get a thick chocolate sauce. Mix this melted chocolate with 1 cup of the muffin batter.
Pour a layer of the banana batter into all of the tins, then top it with a chocolate layer. Continue alternating layers until all the muffin tins are full with the batter. I made the top layer half-banana and half-chocolate. Run a toothpick on top to create a swirl pattern.
Bake the muffins for 22-25 minutes or until a toothpick comes out clean.
Store any leftovers in room temperature in an airtight container.