Preheat oven to 350°F/175°. Grease a muffin pan or line with muffin liners. Set aside.
Make Cream Cheese Swirl. In a medium bowl, beat cream cheese with sugar until smooth and no streaks remained. Add in egg yolk and vanilla extract and beat until well combined.
Make Pumpkin Muffins. In a large bowl, whisk the flour, salt, baking soda and spices together until combined. Set aside.
In a medium bowl, whisk together eggs, granulated sugar and brown sugar until combined. Add oil, yogurt, vanilla extract and pumpkin puree and whisk until combined. Slowly pour the wet mixture into the flour mixture and gently mix just until just combined, there are no lumps remained.
Scoop out the batter into muffin cups using the ice cream scoop, filling about 3/4 cup. Top each muffin with about 1 tablespoon of cream cheese mixture and make the swirl using a toothpick. Bake muffins for 18-20 minutes, or until a toothpick inserted in the center comes out clean. Remove from the oven. Allow to cool for 10 minutes in the pan, then transfer to a wire rack to cool completely.
Muffins are served best the same day they are made, but can be kept in an airtight container in the fridge for up to 3 days and stays frozen for up to 2 months. Serve them at room temperature.