Extra pretzels and mini peanut butter cups,for garnish, if desired
Preheat oven to 350 degrees F.
In a medium bowl, whisk together the flour, baking soda, and salt. Set aside.
In the bowl of a stand mixer, use the paddle attachment to beat the butter and sugars together until smooth, about one minute. Scrape down the side of the bowl with a spatula. Add the peanut butter and mix until smooth, about another minute.
Scrape down the sides of the bowl again and add the eggs and vanilla extract. Mix until combined.
With the mixer off, add in all of the dry ingredients. Turn the mixer on low and mix until just combined. Stir in the chopped pretzels, mini peanut butter cups, and chocolate chips.
Portion dough with a cookie scoop or spoon, about 2 tablespoons of dough per cookie. Roll the cookie dough balls into the extra 1/3 cup of granulated sugar so they are well coated. Place onto a baking sheet that has been lined with parchment paper or a Silpat baking mat, about 2 inches apart.
Bake the cookies for 10 to 12 minutes or until golden brown around the edges, but still soft in the middle. Remove from the oven and sprinkle the cookies with flaky sea salt. You can also gently press additional pretzels and mini peanut butter cups on top for looks, if desired. Let the cookies cool on the baking sheet for 5 minutes. Transfer to a cooling rack and cool completely.
If you can't find mini peanut butter cups, you can chop up regular peanut butter cups.