Preheat oven to 375°F. Place paper baking cups into muffin pan. Set aside.

In a medium bowl, whisk flour, pumpkin spice, baking soda, and salt until well combined. Set aside.

In a large bowl, whisk together pumpkin, sugar, and brown sugar. Beat in eggs, vegetable oil, and vanilla extract. Slowly whisk in the flour mixture until there are no lumps. Fill muffin tins 3/4 full.

In a medium bowl, beat cream cheese until smooth. Add in sugar, egg yolk, and vanilla extract; beat until well combined.

Top each muffin with about 1 tablespoon of cream cheese mixture and use a toothpick to swirl it into the batter.

Bake muffins for 18 to 20 minutes, or until a toothpick inserted in the pumpkin part comes out clean with just a few moist crumbs stuck to it. Let cool for 10 minutes, then serve warm or let cool completely to store.