Pre-heat the oven to 375°F. Line the muffin plan with paper liners and set aside.
In a large bowl, whisk together the flour, pumpkin pie spice, baking soda and salt. Set aside.
In a large bowl, gently whisk together the pumpkin puree, granulated sugar and brown sugar.
Slowly beat in the eggs, vegetable oil and vanilla extract.
Slowly whisk in the dry flour mixture, until you've worked out the lumps.
Fill the muffin tins about 3/4 of the way full.
In a large bowl, beat the cream cheese until smooth. Slowly beat in the granulated sugar, egg yolk and vanilla extract until combined.
Drop about 1 tablespoon of the cream cheese frosting to the tops of each muffin.
Using a toothpick, gently swirl the cream cheese frosting into the batter.
Bake the muffins for 18-20 minutes.
Enjoy once cooled!