Preheat oven to 350 degrees F.

Sift flour, baking soda, and salt in a medium bowl. Set aside.

In the stand mixer bowl, beat the butter and sugars together until smooth for one minute. Scrape the bowl, Add the peanut butter and mix until smooth, about another minute.

Scrape down the bowl again and add the eggs and vanilla extract. Mix until combined.

Without the mixer on, add the dry ingredients. Turn the mixer on low and mix combined. Stir in pretzels, mini peanut butter cups, and chocolate chips.

Portion dough with a cookie scoop, about 2 tablespoons for each cookie. Place onto a baking sheet that has been lined with parchment paper 2 inches apart.

Bake the cookies for 12 minutes. They will be light brown around the edges but still soft in the middle. Sprinkle the cookies with flaky sea salt. 

Let the cookies cool for a few minutes. Then, transfer to a wire rack and cool completely.