Preheat oven to 350
Add the flour, sugar, baking powder, baking soda, pumpkin pie spice, nutmeg, and salt into a bowl and whisk together. Set aside while you work on the next step.
In another separate bowl, mix together the pumpkin puree, egg, and melted butter. Make sure the melted butter is cooled down. Add in the vanilla extract and mix until combined. Add the wet ingredients to the dry ingredients and mix. Make sure you don’t over mix the batter. Make sure it's just blended together; there's no need to mix for more than 5 minutes.
Now let’s prepare the filling. Using a mixer or by hand, mix up the cream cheese, sugar, flour, milk, and vanilla extract until combined. Add this filling to a piping bag or if you don’t have a piping bag, use a ziploc bag and cut the corner out. I always do it this way. Dip the bag filled with filling into each muffin filling it with cream cheese. Dip the piping bag into the center of the muffin batter and slowly lift it up to the top of the muffin. This lady is annoying so be patient.
Bake for 25 minutes and check if the muffins are ready by poking with a toothpick. Let the muffins cool slightly before removing them from the muffin pan.