Preheat the oven to 375°F. Place paper baking cups into the muffin pan. Set aside.

In a medium bowl, whisk together the flour, baking powder, salt, and pumpkin pie spice. Set aside.

In a large bowl, whisk together the pumpkin, brown sugar, granulated sugar, eggs, vegetable oil, and vanilla.

Whisk the flour mixture into the pumpkin mixture, mixing until combined and smooth. Do not overmix.

In a medium bowl, beat the softened cream cheese until smooth. Add the sugar, egg yolk, and vanilla and beat until well combined and smooth.

Put the filling in a small sealable bag and snip off a small portion of the corner (make a snip about ¼-inch wide, but no bigger). Set it aside.

Fill muffin tins ⅓ full with pumpkin batter. Add to this a thin layer of filling (about 1 tablespoon). Add more pumpkin batter almost to the top. Drizzle a little more filling over the batter in a circular pattern.

Use a toothpick to gently swirl the filling with the pumpkin. Don't mix too much, or it will all blend together. Each muffin tin should be full to get that nice dome top.

Bake for 20 to 25 minutes. Insert a toothpick in the center of one muffin. If the toothpick comes out clean, the muffins are done.

Allow them to cool for 10 minutes, then remove the muffins from the pan to finish cooling on a cooling rack.

Store in an airtight container in the fridge. If you want them warmed up after being in the refrigerator, heat them in the microwave for about 15 - 20 seconds.