Preheat oven to 350°F. Spray a 12-cup muffin pan with cooking spray.
Mix the bananas, milk, eggs, oil, and vanilla together in the bowl of a stand mixer until combined. Add the sugar and continue to mix until combined.
Whisk the flours, flaxseed, baking soda, cinnamon, and salt together in a medium bowl. Add the dry ingredients to the wet ingredients in the mixer and beat until just combined (do not over-mix). Stir the chocolate chips into the batter.
Pour the batter into the prepared muffin pan. Bake in the oven for 20-25 minutes, or until a toothpick inserted into the center comes out clean. Remove from oven and cool for 10 minutes in the pan on a wire rack. Remove the muffins and cool completely on wire rack.