Preheat the oven to 375 degrees F. Line a large muffin tin with paper muffin liners and set aside.
Add the flour, baking soda, baking powder, salt, cinnamon and nutmeg to a large mixing bowl and whisk to combine.
Peel the bananas and add them to a separate large bowl. Use a fork to mash them into a chunky paste. Then add the brown sugar, coconut oil, Greek yogurt, eggs, and vanilla to the bananas and whisk to combine.
Add ½ of the banana mixture to the dry ingredients and mix to combine. Add the chocolate, followed by the rest of the banana mixture and mix until the batter just comes together.
Use a ¼ cup measure to fill each well of the muffin tin with the batter. Make sure to only fill the batter to ¾ of the well, to allow the muffins to rise as they bake. Top each muffin with a pecan half (if desired) and bake for 22-25 minutes, or until a toothpick inserted into the center of the muffins comes out clean.
Serve warm from the oven and enjoy!