Preheat oven to 375°F. Place paper baking cups into muffin pan or spray muffin wells with cooking spray. Set aside.

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

In large bowl, whisk together pumpkin, sugar and brown sugar. Mix in eggs, oil and vanilla extract. Slowly whisk in the flour mixture, until there are no lumps. Fill muffin tins evenly. Using a large cookie scoop makes it easy.

In a medium bowl, beat cream cheese until smooth. Add in sugar, egg yolk and vanilla extract and beat until well combined. This is easier done in a stand mixer, but you can mix it by hand with a whisk if your cream cheese is soft enough.

Top each muffin with about small spoonful (I use the small cookie scoop) of cream cheese mixture and use a toothpick to swirl it into the batter.

Bake muffins in preheated oven for 22-25 minutes, or until a toothpick inserted in the center comes out clean. Do not open the oven to check on them until they are nearing the end of their cooking time.