Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or grease the cups well.

In a medium bowl, whisk together the almond flour, coconut flour, 1/4 cup of the granular sweetener, baking powder, pumpkin pie spice, cinnamon, and salt.

In a large bowl, whisk together the pumpkin puree, eggs, almond milk, melted coconut oil or butter, and 1 teaspoon vanilla until smooth.

Add the dry ingredients to the wet ingredients and stir until just combined. Let the batter rest for 3 to 5 minutes so the coconut flour can absorb some of the moisture.

In a small bowl, beat the cream cheese, egg yolk, powdered sweetener, remaining 1/4 cup granular sweetener, and 1/2 teaspoon vanilla until smooth and creamy.

Divide the muffin batter evenly among the prepared muffin cups, filling each about 3/4 full.

Add about 1 teaspoon of the cream cheese mixture to the top of each muffin, then use a toothpick or skewer to gently swirl it into the batter.

Bake for 20 to 24 minutes, or until the muffins are set and a toothpick inserted into the pumpkin portion comes out mostly clean.

Cool the muffins in the pan for 10 minutes, then transfer them to a wire rack to cool completely before serving.