Preheat your oven to 350°F (175°C). Grease your muffin tins well with non-stick spray or butter to make sure the cookie cups release easily later.
In a medium bowl, whisk together 2 cups all-purpose flour, ¼ cup Dutch-processed cocoa powder, ¼ cup black cocoa powder, 1 teaspoon baking soda, and ½ teaspoon salt. This cocoa combo gives the cookie cups a deep, rich chocolate flavor.
Using your mixer, beat 1 cup softened unsalted butter with ½ cup granulated sugar and 1 cup packed light brown sugar until the mixture is light and fluffy — about 3-5 minutes. This step is crucial for that tender cookie texture.
Beat in 2 large eggs, one at a time, then add 1 teaspoon vanilla extract. Mix until fully incorporated.
Gradually add the dry ingredient mixture into the wet ingredients, mixing just until combined. Be careful not to overmix or your cookies will be tough.
Scoop the cookie dough into each muffin cup, pressing down slightly to form a small well in the center for the cheesecake filling later. Make sure the dough spreads evenly along the sides and bottom for sturdy cups.
Bake for 10–13 minutes until the edges are set but the centers are still soft. Remove from oven and immediately press the back of a spoon into the center of each cookie to deepen the wells while the dough is warm. Let cool in the pan for 10 minutes, then transfer to a wire rack to cool completely.