In a medium bowl, whisk together 1 1/4 cups all-purpose flour, 1 teaspoon baking soda, and 2 teaspoons kosher salt. Set aside.
In the bowl of a freestanding electric mixer fitted with a paddle attachment, combine 1/2 cup unsalted butter, 1/2 cup dark brown sugar and 6 tablespoons granulated sugar. Beat on medium-high speed until light and fluffy, at least 5 minutes. When the mixture is light and fluffy, lower the mixer speed to its lowest setting and add 1 large egg and 1 teaspoon pure vanilla extract. Continue mixing on low speed and add the dry ingredients (from the 2nd step), mixing until just incorporated. Add 1 1/2 cups semisweet chocolate chunks — be careful NOT to overmix. At this point, it's okay to have one or two flour streaks left in the batter.
Once the chocolate chunks have been dispersed throughout the dough, turn off mixer. Add 1 cup mini peanut butter cups to the dough, and use a spatula to mix them into the dough. Cover the bowl with plastic wrap and refrigerate until the dough is completely chilled, at least one hour.
Once the dough has been chilled, center a rack in the oven and preheat o 350 (F). Prepare 2 baking sheets by lining with parchment paper.
Use a 1-tablespoon cookie dough scoop to measure out heaping dough balls onto the parchment-lined baking sheets, spacing each dough ball at least 3 inches apart. Use your palms to roll each dough ball into a circle.
Bake the cookies until the bottoms and edges are lightly browned and the tops feel firm, about 13 minutes. In my oven, only one cookie sheet will fit at a time — place the other cookie sheet in the fridge to chill while the other bakes. When the cookies are finished baking, transfer the cookie sheets to a wire rack and allow to cool completely.
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