Preheat your oven to 375°F and line a muffin tin with paper liners.
In a medium bowl, whisk together flour, pumpkin pie spice, cinnamon, salt, and baking soda.
In a large bowl, whisk the eggs, sugar, pumpkin puree, oil, and vanilla until smooth.
Add the dry ingredients to the wet and stir until just combined—don’t overmix.
In a small bowl, beat together the cream cheese, sugar, egg yolk, and vanilla for the swirl mixture.
Spoon the pumpkin batter evenly into the muffin cups, about 3/4 full.
Drop a spoonful of cream cheese mixture on top of each and use a toothpick to swirl gently.
Bake for 18–20 minutes or until a toothpick comes out mostly clean from the muffin part.
Cool in the pan for 5 minutes, then move to a wire rack to cool completely.