Preheat oven to 350°F (175°C) and line a muffin pan with liners.
In a bowl, whisk flour, pumpkin pie spice, cinnamon, baking soda, and salt.
In another bowl, beat eggs, sugars, pumpkin puree, oil, milk, and vanilla until smooth.
Mix dry ingredients into wet ingredients just until combined.
In a small bowl, beat cream cheese, sugar, and vanilla until creamy.
Fill muffin liners ¾ full with pumpkin batter.
Spoon about 1 tbsp of cream cheese filling into the center of each muffin.
Sprinkle tops with pepitas.
Bake for 18–22 minutes or until a toothpick comes out clean (not through cream cheese).
Cool in the pan for 10 minutes, then transfer to a wire rack