Make the dough

1. Brown the butter: Melt the butter over medium low heat in a skillet until the foaming subsides and you see brown flecks in the butter. It will smell nutty. Chill the brown butter in the freezer for 20 minutes.
2. Preheat the oven to 375 F (190 C).  Line sheet pans with parchment

   (Affiliate)

   paper.
3. Prep the mix-ins: Cut up the dark chocolate into squarish/rectangularish pieces about 1/2″ wide. Set aside 20 big chunks of chocolate and 20 whole pretzels for the tops of the cookies. Break up the rest of the pretzels into about 8 pieces each.
4. Mix the dry ingredients: Whisk the flour with the arrowroot

   (Affiliate)

   starch, baking soda, and salt. Dump in the chocolate chips and stir to distribute the chips through the flour.
5. Mix the sugars: Mix the sugars with the cold-ish brown butter (some will still be liquid, and that’s just fine) just until it turns into a sandy paste. You don’t want to incorporate too much air, or the cookies could collapse in the oven.
6. Add in the liquid ingredients: Add the egg, egg yolk, vanilla, and heavy to the sugar. Mix just until everything is smooth. 
7. Add in the flour/chocolate: Mix in the flour, white chocolate chips, dark chocolate chunks, and pretzel pieces into the sugar paste just until the flour disappears.  The dough needs to just stick together.  It may seem dry, but it will bake up into perfectly craggy cookies once all is said and done, especially if you live at high altitude.

Bake the cookies

1. Scoop 2 ounce balls of dough (6/sheet) onto parchment

   (Affiliate)

   lined baking sheets. Rough up the outsides of the cookies by pulling each dough ball apart and sticking the outsides together.  Doing so will make the dough balls look a little more craggy and less perfect, which is ideal for a cookie like these pretzel chocolate chip cookies that are all about texture.
2. Top each cookie with a piece of the reserved chocolate and 1 whole pretzel.  Be sure to press down a little on the pretzel to adhere it to the top of the cookie.
3. Bake the cookies for 12 minutes, 2 sheet trays at a time, rotating the sheets top to bottom and back to front halfway through baking. Repeat with the rest of the dough.

Make the caramel and finish the cookies

1.  While the cookies are baking, follow the recipe for Coffee caramel sauce.  If you don’t want to make homemade caramel, unwrap the soft caramel candies and melt them in a microwaveable cup.
2. Drizzle: As soon as the cookies come out of the oven, drizzle them with a spoonful of the caramel sauce. If the caramel gets a little too stiff by the time the second batch of cookies comes out of the oven, warm it for a few seconds on the stove (or the microwave if you’re using soft caramel candies).
3. Cool: cool the cookies on the tray they baked on.  Cookies are best when they are warm, but you can store them in an airtight container at room temperature for up to 5 days.  You can also freeze the cookies for about 2 months.