In a large bowl, combine flour, pumpkin pie spice, baking powder, cinnamon, baking soda, nutmeg and salt.
In a separate large bowl, stir/whisk together pumpkin puree, sugars, vegetable oil and eggs. Pour wet mixture over dry ingredients and stir until combined.
Scoop about 1/4 cup or slightly less batter into each muffin liner. Drop 2 teaspoons cream cheese filling into the center of each cup. Top with remaining batter to completely cover the filling. Place into oven and bake for about 18 minutes, or until a toothpick inserted in center comes out clean. Remove from oven and cool completely before frosting.