Preheat the oven to 350F. Fill a standard muffin pan with liners.
Combine the coconut flour, almond flour, cinnamon, nutmeg, baking soda, and salt in a bowl.
In the bowl of a food processor, pulse together the eggs, honey, vanilla, and coconut oil until well combined.
Add the dry ingredients to the wet and pulse to combine.
Allow the mixture to sit for 3-5 minutes for the coconut flour to absorb the liquids. Add the apple cider vinegar, banana, and pulse to combine.
Scoop the batter into the lined muffin pan. Bake for 20-25 minutes until a toothpick inserted into the center of each muffin comes out clean. Cool and enjoy! Keep leftover muffins in the refrigerator.