Preheat the oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease well. For tall muffin tops, leave one cup empty between liners if you have two pans.

In a bowl, beat the softened cream cheese, sugar, egg yolk, vanilla, and a pinch of salt until smooth and creamy. Set aside.

In a large bowl, whisk flour, granulated sugar, brown sugar, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves. Break up any brown sugar clumps with your fingers if needed.

In a separate bowl or large measuring cup, whisk eggs, pumpkin puree, oil, milk, and vanilla until smooth.

Pour wet ingredients into dry ingredients and fold with a spatula until just combined. Do not overmix; a few streaks are fine.

Spoon about 2 tablespoons of batter into each liner (roughly half full). Add a heaping tablespoon of the cream cheese mixture on top. Cover with another tablespoon of batter.

Using a toothpick or butter knife, gently swirl the top to create a marbled look. Aim for the top layer.

Sprinkle coarse sugar if using.

Bake for 18–22 minutes until the tops spring back and a tester comes out with a few moist crumbs. Start checking at 16 minutes if your oven runs hot.

Let the muffins rest in the pan for 5 minutes, then transfer to a wire rack. Let cool for at least 15 more minutes before serving.

Enjoy warm or at room temperature. Pair with a latte or black coffee.