Preheat your oven to 400°F (200°C) and line a 12-cup muffin pan with paper liners.

In a large mixing bowl, whisk together the dry ingredients: flour, baking soda, baking powder, spices, and salt.

In a separate bowl, whisk together the wet ingredients: sugars, eggs, pumpkin puree, vegetable oil, milk, and vanilla extract until smooth.

Gently fold the wet mixture into the dry ingredients until just combined.

In another bowl, beat the cream cheese until smooth, then mix in powdered sugar, egg yolk, and vanilla until creamy.

Fill each muffin cup with pumpkin batter, then add 1 tablespoon of cream cheese filling in the center.

Bake for 5 minutes at 400°F, then reduce to 350°F (175°C) and bake for an additional 15-18 minutes until a toothpick comes out clean.

Allow muffins to cool in the pan for 5 minutes before transferring them to a wire rack.