Beat the cream cheese with the powdered sweetener, cream and vanilla extract until smooth. Set aside.
Preheat the oven to 325F and line a muffin tin with parchment or silicone liners.
In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
Add the eggs, pumpkin puree, melted butter, almond milk, and vanilla extract. Mix until well combined.
Drop a spoonful of batter into the bottom of prepared muffin tins and use a spoon to make a well in the center. Drop a tablespoon of cream cheese filling into the well, then top with more batter to cover the cream cheese mixture
Bake 23 to 25 minutes, or until tops are set and edges are just browned. Let cool in pan 15 minutes before transferring to a wire rack to cool completely.