Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners.

In a medium bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, baking soda, cinnamon, nutmeg, ginger, and salt.

In a large bowl, mix the pumpkin puree, granulated sugar, brown sugar, vegetable oil, eggs, and 1 teaspoon of vanilla extract until well combined.

Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Do not overmix.

In another bowl, beat the softened cream cheese with powdered sugar and 1 teaspoon of vanilla extract until smooth and creamy.

Scoop a tablespoon of the muffin batter into each muffin cup, then add a small dollop of the cream cheese mixture on top. Cover with another tablespoon of muffin batter to seal the cream cheese inside.

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 tin for 5 minutes before transferring them to a wire rack to cool completely.