Preheat the oven to 350° Fahrenheit and line two cookie sheets with parchment paper.
In a medium bowl, whisk together all dry ingredients except the chocolate chunks and crushed pretzels.
In a stand mixer fitted with the paddle attachment, cream the butter and brown sugar on low speed until light and fluffy, about 2–3 minutes.
Add the eggs and nut butter, and mix until well combined.
Add the dry ingredients in thirds, mixing until just incorporated.
Fold in the chocolate chunks and crushed pretzels. (If the dough is too soft to scoop, chill it for 20 – 30 minutes to firm up.)
Scoop 3-tablespoon-sized balls of dough onto a prepared baking sheet, spacing about 9 balls of cookie dough per sheet. Lightly press each ball down. (For more uniform cookies, weigh each dough ball to 40 grams.)
Top with a few extra chocolate chunks and pretzel pieces.
Bake for 8 – 10 minutes, until the edges are set and centers are still slightly gooey. They'll firm up as they cool.
If desired, use a wide cup to gently scoot the cookies into perfect circles right after baking.
Notes
Please double check amounts when using the multiplying feature in the recipe card.
If the dough is a bit wet to roll the cookies, you can put the batter in the fridge for 20 - 30 minutes.
You can add the chocolate chunks and the pretzels into the dough and mix it all together, but I prefer to mix in 1 cup of chocolate chunks while reserving 1⁄4 cup of chocolate chunks to add to the top of the cookies. I add a few pretzel bites to each cookie individually, as well.
Store at room temperature in an airtight container for 3 - 4 days. Freeze baked cookies flat in one layer in a Ziplock bag.
You can also freeze dough balls. Place cookie dough balls on a parchment lined baking sheet and freeze for 30 minutes or so. Then place frozen dough in a Ziplock bag. Bake at the same temperature. Just place on parchment lined baking sheet.