Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
In a medium bowl, whisk together flour, baking soda, baking powder, salt, and pumpkin pie spice.
In a separate large bowl, whisk pumpkin puree, oil, granulated sugar, brown sugar, eggs, and vanilla until smooth.
Gradually add the dry ingredients to the wet ingredients, stirring just until combined. Do not overmix.
In another bowl, beat cream cheese, sugar, egg yolk, and vanilla until smooth and creamy.
Fill each muffin liner about two-thirds full with pumpkin batter.
Add a spoonful of cream cheese mixture to the center of each muffin.
Bake for 18–22 minutes, or until a toothpick inserted into the pumpkin portion comes out clean.
Let cool in the pan for 5–10 minutes before transferring to a wire rack to cool completely.