In a medium bowl, mix flour, baking soda, baking powder, salt, cinnamon, and sugar. Add vegetable oil, vanilla, eggs, pumpkin, and banana, stirring until combined.
Gently fold in about 1 1/2 cups of chocolate chips. Fill each muffin cup about 3/4 full, sprinkle the remaining chocolate chips on top, and place the tray in the preheated oven.