Preheat Oven: Set oven to 375°F (190°C) and line muffin pans with paper liners.
Mix Dry Ingredients: In a medium bowl, whisk flour, baking powder, salt, and pumpkin pie spice.
Mix Wet Ingredients: In a large bowl, whisk pumpkin puree, brown sugar, granulated sugar, eggs, oil, and vanilla until smooth.
Combine: Gently fold dry ingredients into the wet mixture. Stir just until combined—do not overmix.
Prepare Cream Cheese Swirl: Beat softened cream cheese until smooth. Add sugar, egg yolk, and vanilla, mixing until creamy. Transfer to a piping bag or small plastic bag with the corner snipped.
Assemble Muffins: Fill muffin liners ⅓ full with pumpkin batter. Pipe about 1 tablespoon of cream cheese mixture over it. Add more pumpkin batter until almost full. Drizzle a small amount of cream cheese on top and swirl gently with a toothpick.
Bake: Bake for 20–25 minutes, or until a toothpick inserted into the pumpkin portion comes out clean.
Cool: Let muffins cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.