Preheat the oven. Heat oven to 350°F. Line muffin pans with paper liners.
Mix the wet ingredients. In a large bowl, whisk together the pumpkin puree, melted butter, milk, and eggs. Whisk in both sugars, vanilla, pumpkin pie spice, and cinnamon until smooth.
Add the dry ingredients. In a separate bowl, whisk together the flour, salt, baking powder, and baking soda. Gently stir into the pumpkin mixture until just combined. Do not overmix.
Make the filling. In a small bowl, beat the cream cheese, powdered sugar, vanilla, and salt until smooth.
Fill the muffin cups. Divide the batter among the liners, filling each about three-quarters full. Pipe or spoon the cream cheese filling into the center of each muffin, pressing it slightly into the batter.
Bake. Bake for 22–30 minutes, or until the tops are set and a toothpick inserted into the pumpkin portion, away from the cream cheese, comes out clean or with a few moist crumbs. *Mine took 25 minutes.
Cool. Let the muffins cool in the pan for 10 minutes, then transfer to a wire rack. Enjoy!