Preheat the oven to 350ºF.
Add all-purpose flour, whole wheat flour, granulated sugar, baking powder, baking soda, pumpkin pie spice, and salt to a large bowl. Mix until combined. Set aside.
In another bowl, whisk together pumpkin puree, egg, melted butter (cooled), and vanilla extract until combined. Then, add these wet ingredients to the dry ingredients. Mix using a rubber spatula or a wooden spoon until just combined. Don't over-mix the batter.
Grease the muffin tin with non-stick cooking spray or line with paper liners. Scoop the batter into the prepared muffin tin. Fill each liner about ¾ full. Set aside.
Prepare the cream cheese filling. In a bowl, whisk together softened cream cheese, granulated sugar, all-purpose flour, milk, and vanilla extract until combined. Then, transfer the cream cheese filling to the piping bag. Fill each muffin with the cream cheese filling: dip the cut tip of the pastry bag into the center of the batter and slowly add the filling and lift the pastry bag to the top of the muffin. You need to add about 1 tbsp of cream cheese filling to each pumpkin muffin.
Bake in a preheated oven for 15-20 minutes or until ready. Check the readiness of the muffins using a toothpick inserted in the muffin (not the filling). Allow muffins to cool slightly before removing from tin.
