Preheat your oven to 350°F. Line a 12-cup muffin tin with paper liners or grease the muffin cups with non-stick spray.
In a small bowl, beat together the softened cream cheese, granulated sugar, and vanilla extract until smooth. Set aside.
In a large mixing bowl, whisk together the flour, granulated sugar, brown sugar, baking soda, baking powder, salt, cinnamon, and pumpkin pie spice.
In a separate bowl, whisk together the eggs, pumpkin puree, vegetable oil, milk, and vanilla extract until well combined.
Pour the wet ingredients into the dry ingredients and mix until just combined. Be careful not to overmix—the batter should be slightly lumpy
Pour the muffin batter into each muffin cup and fill 3/4 of the way. Fill each muffin with the cream cheese filling: push the cut tip of a pastry bag into the center of the batter and slowly add filling. You need to add about 1 tbsp o cream cheese filling.
Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center of a muffin (away from the cream cheese) comes out clean or with a few moist crumbs.
