Spray a 12 cup muffin tin with cooking spray, or line with cupcake papers.
Add all dry ingredients to a sifter or fine mesh sieve. Sift into a bowl.
In a second bowl, whisk together all wet ingredients until well mixed.
Add the wet ingredients to the dry ingredients. Using a mixing spoon or rubber spatula, quickly mix the dry and wet ingredients together until just mixed. Leave a few lumps, and do not over mix.
In a third bowl, add the cream cheese, powdered sugar, and vanilla extract. Using an electric mixer, beat until smooth. Set aside.
Fill each muffin cup halfway with pumpkin batter. Use a spoon to make an indentation in the center of each muffin. Spoon about 1-1.5 tablespoons of cream cheese filling into the indentation. Top off with remaining pumpkin batter, so that each muffin cup is nearly full.
Use a butter knife or toothpick to carefully swirl the cream cheese with the pumpkin batter. Don't mix the cream cheese in completely, just a few swipes is enough.
Place muffins in the oven and set timer for 5 minutes. Leaving the muffins in the oven, reduce oven temperature to 350 degrees. Bake for another 20-25 minutes, or until a toothpick inserted into the center of the muffin comes out clean.
Remove muffins from muffin tin as soon as possible and allow to cool on a wire rack.