Preheat oven to 350 degrees F. Line a large baking sheet with a Silpat baking mat or parchment paper. Set aside.
In a medium bowl, whisk together flour, cocoa, baking soda, and salt. Set aside.
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.
Add the dry ingredients and mix on low until just combined.
With a spatula, stir in the peanut butter cups, peanut butter chips, and chocolate chips.
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.
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.
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.
Transfer to a cooling rack and cool completely. Store the cookies in an airtight container for up to 3 days.