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

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

In another bowl, combine the granulated sugar, brown sugar, pumpkin puree, eggs, vegetable oil, and 1 teaspoon of vanilla extract. Mix until smooth.

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

In a small bowl, mix the softened cream cheese, powdered sugar, and 1/2 teaspoon of vanilla extract until creamy and smooth.

Spoon about 1 tablespoon of the muffin batter into each muffin cup, followed by a teaspoon of the cream cheese mixture, and then top with another tablespoon of muffin batter.

Use a toothpick or knife to gently swirl the cream cheese filling into the muffin batter for a marbled effect.

Bake in the preheated oven for 18-20 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.