First Preheat your Oven to 350F and line a muffin tin with cupcake liners.
In a large bowl, mix flour, with baking soda, baking powder, and spices. Set Aside.
In another medium-sized bowl mix Pumpkin Puree, canola oil, milk, egg and vanilla. Once everything is properly mixed, add it to your dry ingredients. Mix lightly with a balloon whisk or a spatula until you get a lumpy batter.
In a bowl, mix cream cheese with sugar and vanilla until light and smooth.
Fill the muffin tins with muffin mixture. Add 1 spoon of cream cheese filling. Top it with some muffin batter. Finally, add one more spoon of cream cheese filling.Use a toothpick to create a swirl on top. Bake these muffins in a preheated oven at 350F for 15-17 minutes until a toothpick inserted at the center comes out with few moist crumbs.
Once it is baked, cool it down in the tin for 5 minutes and then on a wire rack for at least 20-minutes. Enjoy!