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

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

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

Gradually add the dry ingredients to the wet ingredients, mixing until just combined.

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

Scoop a tablespoon of pumpkin muffin batter into each muffin cup, followed by a dollop of the cream cheese mixture, and then top with another tablespoon of muffin batter.

Use a toothpick or skewer to gently swirl the cream cheese filling into the muffin batter.

Bake in the preheated oven for 20-25 minutes, or until a toothpick inserted into the center comes out clean.

Remove from the oven and let cool in the pan for 5 minutes before transferring to a wire rack to cool completely.