Preheat oven to 350°F (175°C) and line a muffin tin with paper liners or grease lightly.
In a large bowl, mash the bananas until smooth. Whisk in eggs, maple syrup, yogurt, coconut oil, and vanilla extract until well combined.
In a separate bowl, whisk together the whole wheat flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
Gradually add the dry ingredients to the wet ingredients and mix until just combined — do not overmix.
Fold in the dark chocolate, reserving a few to sprinkle on top.
Divide the batter evenly among the muffin cups, filling each about 2/3 full.
Sprinkle the reserved chocolate on top of the batter.
Bake for 18-22 minutes, or until a toothpick inserted in the center comes out clean.
Allow muffins to cool in the tin for 5 minutes before transferring to a wire rack to cool completely.