Preheat oven to 350 degrees F (175 degrees C). Spray 12 muffin cups with cooking spray.
Combine bananas, flour, oats, eggs, wheat germ, maple syrup, coconut oil, ground flax seed, cinnamon, vanilla extract, baking powder, baking soda, and sea salt in a large bowl until batter is well mixed; fold in cranberries and pecans. Fill muffin cups with batter.
Bake in the preheated oven until a toothpick inserted in the center comes out clean, 25 to 28 minutes.