Preheat the oven to 400°F. Coat bottoms of a 12-cup muffin tin with cooking spray and set aside.
In a large bowl, combine flours, millet, baking powder and salt.
In another bowl whisk together milk, mashed banana, eggs, applesauce, brown sugar, and vanilla. Add to flour mixture all at once. Stir just until moistened; do not overmix (batter should be lumpy). Fold in chopped banana.
Fill muffin cups 2/3 full with batter. Bake for 15-18 minutes, or until golden. Cool in tin for 5 minutes, then remove to a wire rack or serve warm.