Preheat oven to 350 degrees F. Line a large baking sheet with a Silpat baking mat or parchment paper. Set aside.: As you prepare the oven it will begin to warm the kitchen with a gentle, dry heat that readies the air for baking, and you may notice a faint hum as the elements come up to temperature. This is important because an evenly preheated oven ensures the cookies spread and set predictably, creating consistent edges and centers. A common mistake is skipping the preheat, which can cause uneven spreading or underbaked middles. Make sure the rack is centered so heat circulates well and the bottoms brown evenly.
In a medium bowl, whisk together flour, cocoa, baking soda, and salt. Set aside.: When you whisk these dry components you release the aroma of cocoa and evenly distribute the baking soda and salt , which prevents pockets of salty or bitter flavor. Visually you should see a uniform brown mixture with no streaks of flour. A typical error here is not fixing glued words from the ingredient list when measuring, so double check measurements and sift if your cocoa or flour is lumpy. Even mixing ensures predictable rise and texture in the final cookie.
In the bowl of a stand mixer, cream together the butter and sugars until creamy and smooth, about 1 minute. Add in the eggs and vanilla extract and mix until combined.: As you cream, you will notice the butter and sugars lighten in color and form a smooth ribbon when lifted with the paddle, trapping air that contributes to a tender cookie. The aroma will shift toward warm caramel from the brown sugar. Avoid over creaming which can cause excessive spread in the oven, and be careful to scrape the bowl so everything is evenly mixed. If your butter is too cold, the mixture will not cream properly and your texture will suffer.
Add the dry ingredients and mix on low until just combined.: At this stage the batter will darken and thicken, and you should stop mixing as soon as streaks disappear to avoid developing gluten from the all purpose flour . Over mixing makes cookies tough rather than tender. You want a cohesive dough that still looks slightly soft and pliable. If you see any dry pockets, fold them gently with a spatula rather than increasing mixer time.
With a spatula, stir in the peanut butter cups, peanut butter chips, and chocolate chips.: Folding in the peanut butter cups and chips distributes little nests of candy through the dough, so you get melty, chewy, and crunchy elements in different bites. Use a spatula to preserve the dough texture and avoid pulverizing the chopped candies. A common oversight is adding too many mix ins which can prevent the dough from holding together, so keep the specified amounts to maintain balance.
Form the cookie dough into balls with your hands or with a cookie scoop, about 1 1/2 tablespoons of dough per cookie. Place on prepared baking sheet, about 2 inches apart. Sprinkle cookies with sea salt.: Rolling the dough into evenly sized balls helps the cookies bake uniformly, and placing them with space allows them to spread into round shapes. You will notice a faint sheen from the butter on the surface; that is normal. The sea salt lightly sprinkled on top will create bright flavor highlights after baking. A frequent mistake is crowding the pan, leading to merged cookies, so keep that spacing consistent.
Bake cookies for 10 to 12 minutes or until cookies are set around the edges but still soft in the center. Don't over bake.: As the cookies bake you will see the edges firm and slightly darken while the centers remain glossier; that visual cue tells you when to pull them. The kitchen will fill with a warm chocolate aroma that intensifies as the sugars caramelize. Over baking will produce dry, hard centers, so aim for that soft middle that continues to set off the hot sheet. Rotate the pan halfway through if your oven has hot spots to ensure even browning.
Let the cookies cool on the baking sheet for 3 to 5 minutes. While cookies are cooling, gently press additional chopped peanut butter cups and chips onto the tops of the cookies. This is optional but will make the cookies extra pretty and extra delicious.: Cooling briefly on the sheet allows the cookies to finish setting without breaking apart, and pressing extra candies while they are still warm helps the pieces adhere without melting completely into runny puddles. The tactile step of pressing candies creates an appealing finished look and a textural top. A common pitfall is waiting too long to press, which may prevent the pieces from sticking properly.
Transfer to a cooling rack and cool completely. Store the cookies in an airtight container for up to 3 days.: Moving the cookies to a rack prevents moisture buildup on the bottoms and preserves the crisp edge and soft center contrast. As they cool, you will notice the interiors shift from glossy to matte, signaling readiness to serve. For storage, an airtight container keeps them fresh but avoid stacking warm cookies which can trap steam and soften edges. If you need longer storage, freeze the baked cookies in a single layer separated by parchment.