Preheat oven to 425°F. Line a standard 12-cup muffin pan with paper liners.

Combine pumpkin puree and both sugars in a large bowl and whisk until smooth and glossy. Add eggs, oil and vanilla and whisk to combine.

Combine flour, pumpkin pie spice, cinnamon, baking powder, baking soda and salt in a medium bowl and whisk to blend evenly. Add dry ingredients to the pumpkin mixture and start to fold them in; before fully incorporated, add the milk and fold until evenly combined. Let the batter rest for 30 minutes.

Meanwhile, make the cream cheese filling by combining cream cheese, sugar, flour and vanilla in a small bowl; blend until smooth. Add milk and mix until combined and smooth. Transfer filling to a piping bag or zip-top bag.

Use a 2 oz scoop to divide batter evenly among prepared muffin cups, filling them to the rim. Snip the tip off of the piping bag and place it into the center of the batter, squeezing to create a swirl at the top.

Sprinkle chopped pumpkin seeds over the batter, pressing in slightly.

Bake at 425°F for 5 minutes, then reduce oven temperature to 350°F. Bake for an additional 12-15 minutes until firm and a toothpick inserted comes out clean.

Let cool in the pan for 5 minutes before transferring muffins to a wire rack.