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

In a large mixing bowl, combine the all-purpose flour, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt. Whisk together until well combined. This ensures even distribution of the leavening agents and spices.

In another bowl, mix the canned pumpkin puree, granulated sugar, brown sugar, vegetable oil, eggs, and vanilla extract. Use an electric mixer on medium speed until the mixture is smooth and well blended. This step incorporates air into the batter, making the muffins fluffy.

Gradually add the dry ingredients to the wet ingredients, mixing on low speed until just combined. Be careful not to overmix, as this can lead to dense muffins.

In a separate bowl, beat the softened cream cheese with the granulated sugar, egg, and vanilla extract until smooth and creamy. This filling will add a deliciously tangy flavor to the muffins.

Spoon a tablespoon of the pumpkin batter into each muffin cup, filling it about ⅓ full. Then, add a tablespoon of the cream cheese filling on top of the batter.

Top with another tablespoon of pumpkin batter, covering the cream cheese filling completely. This layering creates a delightful surprise in each muffin.

Bake in the preheated oven for 20-25 minutes, or until a toothpick inserted into the center comes out clean. The muffins should be golden brown on top.

Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely. This helps maintain their moisture.