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 powder, 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.
Place the ingredients for the cheesecake mixture into a medium bowl and whip using a handheld mixer. Mix for 30-40 seconds or until smooth.
Spoon the chocolate batter evenly into the paper liners. Fill about 3/4 of each liner with batter. To the top of the batter, add about a tablespoon of the cheesecake mixture. Swirl together with a fork or a toothpick.
Bake until a toothpick inserted into the center of a muffin comes out clean, 22-25 minutes, or until a toothpick comes out clean. Remove the muffins from the oven and transfer them 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