Preheat your oven to 350°F (175°C). Line a muffin tin with paper liners or grease it with cooking spray.

In a large mixing bowl, whisk together the all-purpose flour, baking soda, baking powder, ground cinnamon, ground nutmeg, and salt until well combined.

In another bowl, combine the pumpkin puree, granulated sugar, brown sugar, vegetable oil, eggs, and vanilla extract. Mix using an electric mixer on medium speed until smooth and well blended.

Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Be careful not to overmix; a few lumps are okay.

In a medium bowl, beat the softened cream cheese with granulated sugar until smooth and creamy.

Add the egg and vanilla extract, mixing until fully incorporated. Set aside.

Spoon a tablespoon of muffin batter into the bottom of each muffin cup.

Add a heaping tablespoon of the cream cheese filling on top of the batter.

Top with another tablespoon of muffin batter, covering the cream cheese filling completely.

In a small bowl, mix the granulated sugar and ground cinnamon for the topping. Sprinkle this mixture evenly over the muffins.

Bake in the preheated oven for 20-25 minutes, or until a toothpick inserted into the center comes out clean.

Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.