Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners or grease with non-stick spray.
In a large mixing bowl, whisk together almond flour, coconut flour, granulated erythritol, baking powder, baking soda, cinnamon, nutmeg, cloves, and salt.
In a separate bowl, combine pumpkin puree, eggs, almond milk, melted coconut oil, and vanilla extract. Whisk until smooth.
Gradually add the wet ingredients to the dry ingredients, stirring until fully incorporated and no lumps remain.
In a small bowl, make the cream cheese filling by mixing softened cream cheese, powdered erythritol, and vanilla extract until smooth.
Fill each muffin cup about 2/3 full with the pumpkin batter.
Spoon a small dollop of the cream cheese filling onto the center of each muffin and use a toothpick or knife to gently swirl it into the batter.
Bake for 20-25 minutes, or until a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out clean.
Allow the muffins to cool in the pan for 5-10 minutes before transferring to a wire rack to cool completely.
Notes
For best results, use room-temperature cream cheese for the filling. Store leftovers in an airtight container in the refrigerator for up to 5 days.