Preheat oven to 375°F (190°C). Grease or line a 12-cup muffin tin.
In a large bowl, whisk together flour, sugars, baking powder, salt, and spices.
In a medium bowl, beat softened cream cheese with sugar, egg yolk, and vanilla until smooth.
In another bowl, whisk pumpkin puree, oil, eggs, and milk until combined.
Fold wet pumpkin mixture into dry ingredients with a spatula until just combined.
Fill muffin cups ¾ full with batter. Spoon about 1 tablespoon cream cheese mixture on top of each.
Swirl cream cheese gently with a knife or toothpick.
Bake 18–22 minutes, or until a toothpick comes out clean. Cool slightly before serving.