Step 1: Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease it lightly.
Step 2: In a medium-sized bowl, whisk together the flour, baking soda, cinnamon, nutmeg, cloves, and salt until evenly distributed. Set aside.
Step 3: In a large bowl, whisk together the granulated sugar, brown sugar, and vegetable oil until combined. Add the canned pumpkin puree, two large eggs, and 1 tsp vanilla extract. Whisk until the batter is smooth and a beautiful orange hue.
Step 4: Gradually add the whisked dry ingredients into the wet mixture. Stir until just combined, being careful not to overmix. A few lumps are fine.
Step 5: In a small bowl, beat the softened cream cheese, ¼ cup granulated sugar, the single egg yolk, and ½ tsp vanilla extract until beautifully smooth and creamy.
Step 6: Spoon the pumpkin batter into your prepared muffin cups, filling each one about halfway. Place a generous dollop of the cream cheese mixture on top of each muffin. Use a toothpick or skewer to gently swirl the cream cheese into the pumpkin batter for a marbled effect.
Step 7: Carefully place your muffin tin into your preheated oven. Bake for 18–22 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Step 8: Allow the muffins to cool in the tin for about 5 minutes before carefully transferring them to a wire rack to cool completely.