Prepare. Preheat your oven to 350°F (175°C). Line your muffin pan(s) with paper liners or lightly grease the cups with nonstick cooking spray.
Dry Ingredients. In a medium bowl, use a whisk to combine together the flour, pumpkin pie spice, baking soda, and salt until evenly combined.
Wet Ingredients. In a large mixing bowl, beat or whisk together the pumpkin puree, a cup of the sugar, a half cup of the brown sugar until combined. Then add the eggs, one at a time, gently mixing between additions, followed by the vegetable oil and the two teaspoons of the vanilla extract. If you are adding the orange gel food coloring, you can stir in a small amount here until the desired color is reached.
Combine Use a rubber spatula or similar item to gradually add the dry ingredients from the first bowl to the pumpkin mixture, stirring just until no dry streaks remain. Avoid overmixing.
Filling In a separate bowl, beat together the softened cream cheese, remaining sugar, the egg yolk, and the remaining vanilla extract until smooth and creamy.
Assemble. Start by spooning enough pumpkin batter into each muffin cup to fill it about one-third full. Add a heaping tablespoon of the cream cheese mixture to the center of each muffin. Cover with additional pumpkin batter until the muffin cups are about three-quarters full. If desired, you can use a toothpick or skewer to gently swirl a small amount of the cream cheese filling into the top of each muffin for a decorative look.
Bake Bake for 20–24 minutes, or until the tops are set and a toothpick inserted into the pumpkin portion of a muffin comes out with a few moist crumbs. Avoid testing directly in the cream cheese center.
Cool. Allow the muffins to cool in the pan for 5–10 minutes before transferring them to a wire rack to cool completely.