Preheat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or lightly grease it.

In a medium bowl, whisk together the flour, baking soda, baking powder, salt, pumpkin pie spice, and cinnamon.

In a large bowl, whisk the eggs, granulated sugar, brown sugar, pumpkin puree, vegetable oil, and vanilla extract until smooth.

Add the dry ingredients to the wet ingredients and fold gently until just combined. Do not overmix.

In a separate bowl, beat the softened cream cheese, sugar, egg yolk, vanilla extract, and salt until smooth and creamy.

Spoon the pumpkin batter evenly into the muffin cups, filling each about two-thirds full.

Add about 1 tablespoon of the cream cheese filling to the center of each muffin cup. Use a toothpick or skewer to lightly swirl the cream cheese into the pumpkin batter if desired.

Sprinkle the tops with mini chocolate chips or chopped pecans if using.

Bake for 18 to 22 minutes, or until the muffins are set and a toothpick inserted into the pumpkin portion comes out mostly clean.

Let the muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely before serving.