Preheat oven to 375°F. Place paper baking cups into muffin pan. Set aside.
In a medium bowl, whisk flour, pumpkin spice, baking soda and salt until well combined. Set aside.
In large bowl, whisk together pumpkin, sugar and brown sugar.
Beat in eggs, vegetable oil and vanilla extract. Slowly whisk in the flour mixture, until there are no lumps. Fill muffin tins 3/4 full.
In a medium bowl, beat cream cheese until smooth. Add in sugar, egg yolk and vanilla extract and beat until well combined.
Top each muffin with about 1 tablespoon of cream cheese mixture and use a toothpick to swirl it into the batter. This will not look smooth, but it will bake up much prettier. (You can see exactly how I did this in the video below.)
Bake muffins for 18 to 20 minutes, or until a toothpick inserted in the center comes out clean. Let cool for 10 minutes, then serve warm or let cool completely to store.
Storage: Store these pumpkin cream cheese swirl muffins in the refrigerator in an airtight container for up to 5 days. I personally like these muffins best served at room temperature or slightly chilled, so I take them out of the fridge for a few minutes before serving to allow them warm up.No Pumpkin Spice? Make your own by combining 4 tsp cinnamon, 2 tsp ginger, 1 tsp cloves, 1/2 tsp nutmeg and 1/2 tsp allspice.Dollop: Don’t have time to swirl the cream cheese into the top of each muffin? Try adding a dollop of the cream cheese filling to the center of the batter instead.Bake A Loaf: If you would prefer to bake a loaf of bread instead of muffins, head over to my pumpkin cream cheese bread. It’s the same recipe, but baked into a loaf!Don’t Over-Mix: Combine the dry ingredients with the wet ingredients gently, just until combined. If you over stir the batter, it can overdevelop the gluten and cause dry muffins.Nutritional Note: Nutrition facts are only estimates. Please be sure to calculate your own nutrition facts with the brands you choose to use for precise measurements.