Prep your pan and oven: Heat the oven to 350°F (175°C). Line a 12-cup muffin pan with liners or grease well.
Mix the filling: Beat cream cheese, sugar, vanilla, and a pinch of salt until smooth and fluffy.
Chill while you make the batter to firm it up slightly.
Combine dry ingredients: In a bowl, whisk flour, baking soda, baking powder, salt, and spices until evenly blended.
Whisk wet ingredients: In a larger bowl, whisk pumpkin puree, both sugars, oil, eggs, vanilla, and milk until smooth.
Bring it together: Add the dry mixture to the wet and stir gently until just combined. Do not overmix; a few small lumps are fine.
Fill the cups: Add about 1 heaping tablespoon of batter to each muffin cup. Spoon 1 tablespoon of cream cheese filling in the center.
Top with another tablespoon of batter to cover. The cups should be about 3/4 full.
Add toppings (optional): Sprinkle with coarse sugar, cinnamon sugar, or a few pepitas.
Bake: Bake 18–22 minutes, until the tops spring back lightly and a toothpick inserted near the edge (not the center of the filling) comes out clean.
Cool: Let muffins cool in the pan for 5 minutes, then move to a rack. Cool at least 15 minutes before eating so the filling sets.