In a mixing bowl, beat the cream cheese, 3 tablespoons of granulated sugar, and 1/2 teaspoon of vanilla extract until the mixture is fluffy and smooth, about 2–3 minutes. Using a small cookie scoop, portion out the filling into balls and place them on a parchment-lined tray. Freeze the cheesecake balls for at least 1 hour until firm.

In a separate bowl, whisk together 6 tablespoons of granulated sugar, 2 1/2 teaspoons of ground ginger, and 2 1/2 teaspoons of ground cinnamon until well combined.

In a large mixing bowl, cream together 3/4 cup of unsalted butter and 3/4 cup of light brown sugar until light and fluffy, about 4–5 minutes. Then, add in 2 egg yolks, 1/3 cup of unsulfured molasses, and the remaining 1 teaspoon of vanilla extract, mixing well until all ingredients are fully combined and the dough is smooth.

In another bowl, sift together 2 1/2 cups of all-purpose flour, 1/2 teaspoon of baking soda, and 1/2 teaspoon of salt along with the remaining spices: 1/2 teaspoon of ground nutmeg, 1/4 teaspoon of allspice, and 1/4 teaspoon of cloves. Gradually mix these dry ingredients into the wet ingredients until just incorporated, forming a soft dough that's slightly sticky.

Preheat your oven to 350°F (175°C) and prepare a baking sheet with parchment paper. Scoop a tablespoon of cookie dough, flatten it on your palm, and place a frozen cheesecake ball in the center. Gently fold the edges over the filling to seal. Roll the formed dough ball in the spiced sugar coating, ensuring it is well coated before placing on the prepared baking sheet.

Carefully transfer the cookies to your preheated oven and bake for approximately 11–12 minutes, or until the edges are set and the tops slightly puffed. Keep an eye on them, as baking times may vary slightly based on your oven.

Once baked, remove the cookies from the oven and let them cool on the baking sheet for about 10 minutes before transferring them to a wire rack to cool completely.