Preheat your oven to 375°F and place paper baking cups into your muffin pan.
In a medium bowl, whisk together flour, pumpkin spice, baking soda, and salt until well combined.
In a large bowl, whisk together pumpkin puree, granulated sugar, and brown sugar. Beat in eggs, vegetable oil (or melted butter), and vanilla extract until well blended. Slowly incorporate the flour mixture until no lumps remain.
In another medium bowl, beat cream cheese until smooth. Add in sugar, egg yolk, and vanilla extract; beat until well combined.
Top each muffin with about one tablespoon of the cream cheese mixture and gently swirl it into the batter.
Bake muffins for about 18 to 20 minutes or until a toothpick inserted into the pumpkin part comes out clean.