Preheat oven to 300 F.
In a medium bowl, combine flour, baking soda, salt, and cocoa powder. Mix well with a whisk or fork and set aside.
2 ½ cups all-purpose flour, 1 teaspoon baking soda, 1 teaspoon salt, ½ cup unsweetened cocoa powder
In a large bowl, beat sugars and butter until well blended. Add eggs and vanilla and beat until light and fluffy.
1 cup brown sugar, ½ cup granulated sugar, 1 cup unsalted butter, 3 large eggs, 1 teaspoon vanilla extract
Add the flour mixture and chocolate chips. Mix on low just until combined. Do not overmix.
6 ounces semisweet chocolate chips
Add 1 tablespoon of dough to each cup in a muffin pan. Place one peanut butter cup in each muffin cup, pushing down cookie dough. Top each peanut butter cup with an additional tablespoon of dough.
24 Reese's peanut butter cups
Bake for 16-18 minutes. Let cool for 1-2 minutes in muffin pan, then gently run a butter knife along the edge of each cookie to loosen. Remove to cooling rack.