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 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 and 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. This will not look smooth, but it will bake up much prettier. (You can see exactly how I did this in the video at the top of the page.)
Bake muffins for 18-20 minutes, or until a toothpick inserted in the center comes out clean.
I liked these best at room temperature or even slightly chilled! Store in an airtight container in the fridge.