Heat oven to 375 degrees. Line muffin tins with liners.
Place the flours, flax, baking powder, cinnamon, baking soda and salt in a large bowl and whisk to combine. Set aside.
In a separate large bowl, place the sugar and butter. With an electric mixer on high speed, beat the sugar and butter until the mixture is light yellow and fluffy. Reduce the speed to medium and add the eggs one at a time, until combined.
Reduce the speed to low and add the banana, quinoa, and yogurt. Mix until just combined. Set the mixer aside. Add the flour mixture and chocolate chips (optional). Using a wooden spoon, stir until just combined. Using a muffin scoop, fill muffin cups about 2/3 full.
Bake 18-20 minutes, rotating pans halfway through cooking time.
Allow to cool in pans for about 10 minutes before removing to a cooling rack.