Preheat the oven to 325°F. Grease or place paper liners in 6 wells of a standard-size muffin pan.

In a large mixing bowl, stir the almond flour, baking soda, salt, and spices until well combined. In another bowl, mix the butter, sweetener, eggs, and pumpkin until smooth. Stir the wet ingredients into the dry. Spoon the batter into the prepared muffin cups, filling each about two-thirds full.

To make the filling, using a hand mixer, beat the cream cheese in a medium-sized bowl until smooth. Add the sweetener, egg yolk, and vanilla and beat until well combined. Top each muffin with about 1 tablespoon of the cream cheese filling and use a toothpick to swirl it into the batter.

Bake the muffins for 30 to 40 minutes, until a toothpick inserted into the center of a muffin comes out clean. Allow to cool before removing from the pan. Store extras in an airtight container in the refrigerator for up to 3 days. Reheat on a baking sheet in a preheated 350°F oven for 5 minutes or until warmed through.