Preheat the oven to 350°F and line a muffin pan with paper liners.
In a medium bowl, beat together the softened cream cheese, powdered Swerve Sweetener, heavy cream, and vanilla until smooth. Set aside.
In a large bowl, whisk together the almond flour, Swerve Sweetener, whey protein powder, baking powder, pumpkin pie spice, and salt.
Add the eggs, pumpkin puree, melted butter, water, and vanilla extract. Mix until the batter is smooth and evenly combined.
Divide part of the batter between the muffin cups.
Add a spoonful of cream cheese filling to the center of each.
Cover with the remaining batter.
Bake for 20 to 24 minutes, until the tops are set and lightly golden.
Cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.