Preheat the oven to 350 degrees.  Spray or line a standard muffin tin and set aside.

In the bowl of a stand mixer, combine the flour, sugar, baking powder, baking soda, pumpkin pie spice, and salt.  Whisk to combine.

In a medium bowl, combine the pumpkin puree, egg, melted butter and vanilla.  Whisk to combine.

Pour the pumpkin mixture into the dry ingredients.  Mix on low speed just until combined.

Divide the batter between the cupcake liners.  Set aside.

To make the cream cheese filling - in the bowl of a stand mixer, combine the softened cream cheese, sugar, flour, milk and vanilla.

Mix on medium low until combined and smooth.

Transfer the filling to a piping bag.  Cut off about ½ of an inch from the tip.

Insert the piping bag just below the surface of the muffin batter and gently squeeze until the filling reaches the top of the muffin (about a tablespoons worth of filling).  Repeat with the remaining muffins.  You can always go back and give some muffins more filling if there is any remaining.

Bake the muffins in the preheated oven for 15-20 minutes or until set and just slightly starting to golden up.

Allow to cool