Preheat your oven to 375°F (190°C) and line a 12-cup muffin tin with paper liners.
In a medium bowl, use an electric hand mixer to beat the cream cheese, 1/4 cup sugar, and 1 tsp vanilla until smooth and fluffy. Set aside.
In a large bowl, whisk together the flour, granulated sugar, brown sugar, pumpkin pie spice, baking soda, and salt.
In a separate bowl, mix the pumpkin puree, eggs, melted butter, and 1 tsp vanilla extract.
Fold the wet ingredients into the dry mixture until just combined; do not overmix.
Scoop a small amount of pumpkin batter into each muffin liner.
Add a teaspoon of the cream cheese mixture on top of the base batter in each liner.
Cover with the remaining pumpkin batter and use a toothpick to gently swirl the surface.
Bake for 18–22 minutes or until a toothpick inserted into the center comes out clean.
Let them cool for 5 minutes in the tin before serving.