Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease the cups lightly.

In a large mixing bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, and cloves.

In a separate bowl, combine the granulated sugar, brown sugar, eggs, pumpkin puree, vegetable oil, and vanilla extract. Mix until smooth.

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

In another bowl, prepare the cream cheese swirl mixture by beating the softened cream cheese, granulated sugar, egg yolk, and vanilla extract until smooth and creamy.

Fill each muffin cup about 3/4 full with the pumpkin batter. Add a small dollop (about 1 teaspoon) of the cream cheese mixture on top of each muffin.

Use a toothpick or skewer to gently swirl the cream cheese mixture into the pumpkin batter without overmixing.

Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.

Remove the muffins from the oven and let them cool in the muffin tin for about 5 minutes. Transfer them to a wire rack to cool completely before serving.