Preheat oven to 350°F (175°C) and line a 12-cup muffin pan with liners.
Beat softened cream cheese with powdered sweetener and vanilla until smooth.
Whisk almond flour, pumpkin pie spice, baking powder, and salt in a bowl.
In another bowl, whisk pumpkin puree, eggs, granulated sweetener, and vanilla. Stir in the dry ingredients until just combined.
Divide batter among the muffin cups. Add a small spoonful of cream cheese mixture to each and gently swirl with a toothpick.
Bake for 20–24 minutes, or until the pumpkin portion is set and a toothpick inserted into the muffin comes out with a few moist crumbs. Cool before serving.