Mix all of the cream cheese filling ingredients until a smooth batter forms.
Preheat the oven to 325F and line a muffin tin with paper liners. You could also use silicone.
In a medium bowl, whisk together the almond flour, sweetener, protein powder, baking powder, pumpkin pie spice, and salt.
Mix in the eggs, pumpkin puree, melted butter, almond milk, and vanilla extract. Mix until well combined.
Add a spoonful of batter into each muffin well, then use a spoon to create a dent for the cream cheese filling in each muffin. Add spoonfuls of filling to the center of each, then top the muffins with a little more batter.
Bake for 25 minutes, or until the muffins are cooked in the middle. Allow to cool before removing the muffins from the tray.