Preheat the oven to 350°F and line a cupcake pan with 12 paper liners.
In a medium bowl, whisk together the cocoa powder, almond flour, coconut flour, baking soda, cream of tarter and salt.
In a large bowl, whisk together the eggs, pure vanilla, almond milk, Monk Fruit Syrup (or Maple Syrup) and melted ghee.
Use a rubber spatula to fold the dry ingredients into the wet ingredients in ¼-cup increments.
Fold in the chocolate chips.
Use a handheld or stand mixer and mix on medium to high speed until all and combine all the ingredients are combined.
Spoon the batter evenly into the paper liners. Fill about 3/4 of each liner with batter.
Bake until a toothpick inserted into the center of a muffin comes out clean, 20 to 25 minutes or until a toothpick comes out clean.
Remove the muffins from the oven and transfer to a rack and allow to cool in the pan for 5 to 10 minutes.
If leftovers, store in an airtight container. Will last up to 1 week