- Preheat oven to 350℉. Line two 12 cup muffin tins with paper liners.
- In a medium bowl, whisk to combine almond flour, coconut flour, baking powder, baking soda, cinnamon, ginger, cardamom, cloves, salt, and pepper.
- In a large bowl, whisk together pumpkin, monk fruit, eggs, vanilla, butter, and milk. Stir in almond flour mixture. Fill muffin tins ⅔ full with batter.
- In a food processor, beat cream cheese until smooth. Add monk fruit, egg yolk, and vanilla and beat until combined.
- Top each muffin with 3 small dollops of cream cheese mixture. Using a toothpick or skewer, swirl the cream cheese into the top of the batter.
- Bake, rotating pans and switching oven racks halfway through baking, for about 30 minutes or until set and well browned on top.
- Let muffins cool in pans for 10 minutes, then transfer to racks to cool completely. Serve immediately or store in an airtight container in the refrigerator for up to 1 week.