Prep. Preheat the oven to 375˚F. Line a 12-cup muffin pan with paper liners and set aside.
Make the cream cheese swirl. In a mixing bowl, beat the cream cheese, sugar, egg yolk, and vanilla with an electric mixer until completely smooth. Set aside.
Combine the dry ingredients. In a large bowl, whisk together the flour, baking powder, baking soda, salt, pumpkin pie spice, cinnamon, and ginger.
Combine the wet ingredients. In another bowl, whisk together the pumpkin puree, eggs, Greek yogurt, melted butter, brown sugar, maple syrup, and vanilla until smooth.
Make the muffin batter. Add the wet ingredients to the dry ingredients and gently fold until just combined. Do not overmix.
Fill the muffin cups. Divide the batter evenly among the muffin cups, filling each about ⅔ full. Spoon about 1½ tablespoons of the cream cheese mixture onto each muffin. Using a toothpick or skewer, gently swirl it into the batter with just 2–3 passes. Sprinkle with the chopped pecans.
Bake. Transfer to the oven and bake the muffins for 20–24 minutes, or until the pumpkin portion is set and a toothpick inserted into the muffin (avoiding the cream cheese swirl) comes out with a few moist crumbs.
Serve. Remove the pumpkin muffins from the oven and let them cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely before serving.
Notes
Bring the cream cheese to room temperature before mixing so you get a nice, smooth swirl.
Avoid overmixing the batter to keep the muffins light, moist, and tender.