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

Make the pumpkin muffin batter. 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 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 but before it is all incorporated, add the milk and fold it in until the batter is evenly combined. Cover the bowl and let the batter rest on the counter for 30 minutes.

Meanwhile, make the cream cheese filling. Combine soft cream cheese, sugar, flour and vanilla in a small bowl and beat with an electric hand mixer or use a wooden spoon to blend until smooth. Add milk and mix until combined and smooth. Transfer the filling to a small piping bag or a 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. Press down to squeeze, pulling up slowly in a circular motion to make a little swirl at the top to fill out about 1-inch diameter circle at the surface of the batter. Sprinkle chopped pumpkin seeds over the pumpkin batter, pressing in slightly.

Bake at 425℉ for 5 minutes. Then, turn the oven down to 350℉. Bake for another 12-15 minutes until they feel firm when pressed and a toothpick inserted comes out clean. Transfer pan to a wire rack and let cool for 5 minutes before transferring muffins individually to the rack to finish cooling.