Preheat your oven to 350°F (175°C) and prepare a muffin tray by lining it with muffin liners or coating with cooking spray.

In a large mixing bowl, whisk together the flour, sugar, baking powder, baking soda, salt, and pumpkin pie spice until evenly combined.

In a separate bowl, mix the pumpkin puree, melted butter, vanilla extract, and egg until smooth and well blended.

Pour the wet ingredients into the bowl with the dry ingredients and stir gently until just combined; do not overmix.

Divide the batter evenly among the muffin liners, filling each about three-quarters full.

To prepare the cream cheese filling, combine the softened cream cheese, sugar, vanilla extract, flour, and milk in a small bowl, mixing until smooth and creamy.

Transfer the cream cheese mixture to a piping bag or a Ziploc bag with a small corner cut off. Pipe a dollop of the cream cheese filling into the center of each muffin cup, allowing it to sink slightly into the batter.

Bake in the preheated oven for 18-20 minutes, or until the muffins are golden and a toothpick inserted into the center comes out clean.

Remove the muffins from the oven and let them cool in the tray for 2-3 minutes before transferring to a wire rack to cool completely.

Serve warm or at room temperature and enjoy!