Combine flours, flaxseed, sugar, baking powder, cinnamon, and salt in a bowl.
Whisk together milk, butter, and eggs in a large liquid measuring cup or small bowl. Add milk mixture to flour mixture, stirring until blended. Fold in mashed bananas.
Preheat a waffle iron. Coat iron with cooking spray. Spoon about 1/4 cup batter onto hot waffle iron, spreading batter to edges. Cook 3-4 minutes or until steaming stops; repeat with remaining batter.