Preheat oven to 375°F and line a muffin tin with paper liners.
In a large bowl, whisk together flour, baking soda, salt, pumpkin pie spice, and cinnamon.
In another bowl, mix pumpkin purée, both sugars, oil, eggs, and vanilla until smooth.
Add the dry ingredients to the wet and stir just until combined—don’t overmix.
In a small bowl, beat cream cheese, sugar, egg yolk, and vanilla until smooth.
Fill each muffin liner about ⅔ full with the pumpkin batter.
Spoon a small dollop of cream cheese mixture into the center of each muffin.
Use a toothpick or knife to gently swirl the cream cheese into the batter.
Bake for 18–22 minutes or until a toothpick inserted near the edge comes out clean.
Let cool in the pan for 5 minutes, then transfer to a wire rack.
