Preheat oven to 350 F. Line a cupcake tin with 12 cupcake liners and set aside.
Combine the flour, cocoa, sugar, baking powder, baking soda, and salt in a large bowl. Set aside. Mash two bananas in the bowl of a mixer with a fork. Attach the bowl to the mixer and add in the egg, vanilla, oil, and milk. Mix well. Slowly pour in the flour mixture and mix until combined. Stir in the chocolate chips.
Scoop out the mixture into the prepared liners until they are 3/4 of the way full. Bake for 20-22 minutes. Cool for 5 minutes in the pan, and then transfer the muffins to a cooling rack to cool completely.