Preheat the oven: Heat oven to 425°F and line a 12-cup muffin pan with liners.
Mix dry ingredients: Whisk flour, baking powder, baking soda, salt, pumpkin pie spice, and cinnamon.
Mix wet ingredients: Whisk sugars, eggs, pumpkin purée, oil, milk, and vanilla until smooth. Fold in the dry ingredients just until combined.
Make the filling: Beat cream cheese, sugar, egg yolk, vanilla, and salt until smooth and creamy.
Fill the cups: Divide pumpkin batter evenly among the muffin liners, filling each about ¾ full to nearly full.
Add cream cheese: Pipe the filling into the center of each muffin, leaving a little visible on top.
Add topping: Sprinkle pepitas and optional coarse sugar around the cream cheese center.
Bake: Bake at 425°F for 5 minutes, then reduce to 350°F and bake for another 15–18 minutes.
Check doneness: Insert a toothpick into the pumpkin crumb beside the filling. It should come out clean or with a few moist crumbs.
Cool: Let muffins cool in the pan for 10 minutes, then transfer to a wire rack before serving.
