Preheat oven to 375°F. Place paper baking cups into muffin pan.
In a medium bowl, whisk flour, pumpkin spice, baking soda and salt until well combined. Set aside.
In the bowl of your mixer, beat together pumpkin, sugar and brown sugar.
Beat in the eggs, vegetable oil and vanilla extract. Slowly add in the flour mixture, until there are no lumps, but being careful not to overmix. 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 creamy.
Top each muffin with about 1 tablespoon of the cheesecake mixture, and use a toothpick to swirl it into the batter.
Bake muffins for 18-20 minutes, or until a toothpick inserted in the center comes out clean.
Store these in a sealed container in the fridge. They can be eaten at room temp, or still chilled.