Preheat oven to 375°F. Grease muffin tins.
Whisk together dry ingredients: flour, pumpkin spice, baking powder, baking soda, and salt.
Whisk wet ingredients: In a large bowl, whisk together pumpkin, sugar and brown sugar. Mix in eggs, oil and vanilla extract.
Slowly whisk the flour mixture into the wet ingredients until there are no lumps. Fill muffin cups evenly about 3/4 full.
Make cream cheese topping: In a medium bowl beat the cream cheese until smooth. Add in sugar, egg yolk, and vanilla extract and beat the mixture until it is fully combined.
Top each muffin with a small spoonful of cream cheese mixture.
Place muffins into the preheated oven and bake for 20-22 minutes, or until a toothpick inserted in the center comes out clean. Allow to cool.