Preheat oven to 375 degrees. Line a muffin pan with paper liners or lightly oil pan.
In a large bowl, mix flour, salt, baking powder, baking soda, cinnamon and pumpkin pie spice until well combined.
In another bowl, whisk together pumpkin puree, egg, oil, milk, vanilla extract, brown sugar and granulated white sugar.
Gently mix dry ingredients into the wet ingredients until just combined.
For the cream cheese layer: In the bowl of your stand mixer; beat together cream cheese, egg, vanilla and sugar until fluffy.
Add a tablespoon of pumpkin mixture to the bottom of each liner. Top with a tablespoon of cream cheese layer, followed by another tablespoon of pumpkin mixture. Swirl top with a toothpick.
Bake muffins in the oven for 18-20 minutes until a toothpick runs through the muffin and comes out clean.
Allow muffins to cool slightly before transferring to a cooling rack. Enjoy!