Preheat oven to 350 degrees.
Line a standard muffin tin with paper cups.
Whisk flours, wheat germ, cinnamon, baking powder, baking soda, and salt in a bowl. Whisk remaining ingredients in a separate bowl. Fold dry ingredients into wet and mix until just combined.
Spoon batter into cups.
Bake until a toothpick inserted in the center of a muffin comes out clean, about 22 minutes. Cool in pan for 15 minutes, then transfer to a wire rack to cool slightly before serving.