Line a muffin tin with cupcake liners, and preheat your oven to 375 degrees Fahrenheit.
In a large mixing bowl, whisk together the pumpkin puree, 1 cup granulated sugar, 1/2 cup brown sugar, 2 eggs, vegetable oil, 2 tsp. of vanilla, and a bit of orange food coloring, if desired.
In a separate bowl, whisk together flour, pumpkin pie spice, baking soda, and salt.
Add the dry ingredients to the wet, folding together with a cake spatula, until well combined.
For the cream cheese, in a medium mixing bowl, beat cream cheese and sugar together until smooth.
Add in the egg yolk and 1 tsp. vanilla extract and mix until well combined.
Fill the cupcake liners 2/3 full with the pumpkin batter.
Add a tbsp. of the cheesecake mixture to each muffin.
Use a toothpick or something similar to swirl the cream cheese mixture and pumpkin batter on top.
Bake for 18-20 minutes.
Allow the muffins to cool and enjoy.