Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt.
In a large bowl, mix the pumpkin puree, vegetable oil, granulated sugar, brown sugar, eggs, and vanilla extract until well combined.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
In a separate bowl, beat the cream cheese, granulated sugar, egg yolk, and vanilla extract until smooth.
Fill each muffin cup with a small amount of batter, then add a spoonful of the cream cheese mixture. Top with more batter until the cups are about ¾ full.
Bake for 20-25 minutes, or until a toothpick inserted into the muffin part comes out clean.
Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.