Preheat oven to 350°F and line a muffin pan with paper liners or grease very well.
In a large bowl, whisk together flour, baking soda, brown sugar, granulated sugar, spices and salt.
In another large bowl, whisk the pumpkin puree, oil, milk and eggs. Make a well in the center of the flour mixture and add pumpkin mixture. Beat until fully combined. Be sure to scrape the bottom of the bowl with a rubber spatula to ensure all dry ingredients are incorporated.
In a small bowl, beat cream cheese until smooth with no lumps. Add vanilla and sugar until smooth.
Add 2 tbs of pumpkin batter to lined muffin pan and top with 1-2 teaspoon of cheesecake filling. Top with more pumpkin batter, filling ¾ to the top.
Bake muffins for 17-20 minutes or until a toothpick inserted in the center comes out with a few moist crumbs. Allow to cool completely in pan.