Preheat the oven to 350 degrees and spray a muffin pan with nonstick cooking spray.
In a large bowl, whisk together 5 eggs, pumpkin puree, melted butter, brown swerve, vanilla extract, and pumpkin pie spice.
Add in almond flour, coconut flour, baking powder, and salt and whisk everything together until smooth. Set this batter aside while you prepare the cream cheese topping.
Using an electric mixer, mix together the cream cheese, egg, and confectioners’ Swerve until smooth.
Scoop the pumpkin batter evenly into the prepared wells of the muffin tin. Top each with the cream cheese mixture, approximately 2 tbsp per each muffin.
Using the tip of a knife or a toothpick, swirl the cream cheese and the pumpkin batter together.
Bake for 22-26 minutes, until the muffins are set.
Let cool completely before serving. Store in an airtight container in the refrigerator for up to 1 week.