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

In a medium bowl, whisk together the gluten-free flour, baking powder, baking soda, salt, cinnamon, nutmeg, ginger, and cloves.

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

Gradually add the dry ingredients to the wet ingredients and mix until just combined.

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

Scoop a tablespoon of the pumpkin muffin batter into each muffin cup, then add a small dollop of the cream cheese mixture on top, followed by another tablespoon of pumpkin batter to cover the cream cheese.

Repeat for all muffin cups, filling them about 2/3 full.

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, then transfer to a wire rack to cool completely.