These cookies are seriously the most decadent treat. The combination of salty, chewy and sweet is divine. Coupled with fresh milled flour, I don’t even feel the least bit guilty about eating more than one of these. These Brown Butter Pretzel, Chocolate Chip Cookies are on regular rotation at our house!
If you’re new to fresh milled flour or unsure what this is, here is some more information to help you get started!
This post may contain affiliate links, please see our privacy policy for details.
Table of Contents

I don’t know about your family, but we love a good gooey cookie. I love to pull them from the oven when they look like there is no way they will hold together with all of the added extras! Sprinkle the with some flaky sea salt and now you have a salty sweet treat! These Brown Butter Pretzel Chocolate Chip Cookies have such a rich, nutty flavor mixed with the crunch and gooey texture, they are unreal!
Ingredients Needed
- Unsalted Butter
- Water
- Coconut Sugar
- Molasses
- Egg
- Vanilla Extract
- Soft White Wheat Flour
- Baking Soda
- Salt
- Chocolate Chips: Semi-sweet or Dark
- Crushed Pretzels
- Flaky Sea Salt for Garnish
Equipment Needed
- Grain Mill
- Stand Mixer
- Digital Scale
- Measuring spoons
- Sheet Pan
- Parchment Paper
- Small Cookie Scoop
- Saucepan
All equipment used in this recipe can be found here!
How to make Brown Butter Pretzel Chocolate Chip Cookies
- First, mill my soft white wheat berries into flour and set aside. Rough chop your pretzels into small pieces, about the size of elbow macaroni.
2. Place your 1/2 cup of unsalted butter in a pan over medium heat for about 5 minutes, until the butter foams and small brown specks appear. Do not step away from your butter as it can burn quickly. Once the butter is a light amber color, remove it from heat and stir in 2 tsp of water to replenish the moisture lost. Transfer to a small bowl to cool to room temperature. This step brings so much flavor to the Brown Butter, Pretzel Chocolate Chip Cookies.

3. In the bowl of a stand mixer, cream together room temperature brown butter with sugar and molasses for a few minutes. Add Egg and Vanilla. Mix until well combined, scraping down sides if needed.
4. Add flour, baking soda and salt. Mix until just combined, careful not to over mix or it will create flat cookies!

5. Carefully fold in chocolate chips and crushed pretzel pieces.
6. Using a 2 TBSP scoop, form cookie balls. Place on a parchment lined sheet pan, leaving 2 inches between the cookies. Place the scooped dough into the refrigerator to chill for at least 20 minutes.
7. While the dough chills, preheat oven to 350 degrees F.
8. Remove chilled dough and place into the hot oven. Bake 11-12 minutes, rotating halfway through. Do not over bake the cookies. It’s actually okay if they are slightly under cooked, they will continue to bake as they cool.
9. Sprinkle with flaky sea salt if you like the additional salt.
10. Once completely cooled, move to an airtight container and store on the counter/fridge for 1 week or freezer for 3 months.

Can I use something other than coconut sugar?
Sure! I do all of my baking with coconut sugar due to the low glycemic index.
If you would like to use cane sugar, I recommend doing half cane sugar, half brown sugar and omitting the molasses.
What does browning the butter do to the recipe?
By browning your butter, you will create a rich, caramelized, nutty flavor!
Could I freeze my dough after scooping?
Yes! They actually do better the longer the dough chills, so freezing them would make an even chewier cookie!
Storing the Brown Butter Pretzel Chocolate Chip Cookies
Once the cookies have cooled completely, transfer them to an airtight container to retain their soft, chewy texture.
Room temperature: 1 week
Freezer: 3 months

Brown Butter Pretzel Chocolate Chip Cookies
Equipment
- 1 Sauce Pan
Ingredients
- 4 oz unsalted butter, browned
- 195 g Soft White Wheat flour
- 275 g Coconut Sugar
- 1 Tbsp Molasses
- 2 tsp water
- 1 large egg
- 1 tsp vanilla extract
- 1/2 tsp baking soda
- 1/4 tsp Redmonds Real Salt
- 1/2 cup chocolate chips
- 1/2 cup chopped pretzels
- Flaky sea salt for garnish
Instructions
- First, mill your soft white wheat berries into flour and set aside. Rough chop your pretzels into pieces the size of elbow macaroni.
- Next, place 1/2 cup (4 oz) unsalted butter in a pan over medium heat for about 5 minutes, until the butter foams and small brown specks appear. Do not step away from your butter as it can burn quickly. Once the butter is a light amber color, remove it from heat and stir in 2 tsp of water to replenish the moisture lost. Transfer to a small bowl to cool to room temperature.
- In the bowl of a stand mixer, cream together room temperature brown butter with sugar and molasses for a few minutes. Add Egg and Vanilla. Mix until well combined, scraping down sides if needed.
- Add flour, baking soda and salt. Mix until combined, careful not to over mix or it will create flat cookies!
- Carefully fold in chocolate chips and crushed pretzel pieces.
- Using a 2 Tbsp scoop, form cookie balls. Place on a parchment lined sheet pan, leaving 2 inches between the cookies. Place the scooped dough into the refrigerator to chill for at least 20 minutes.
- While the dough chills, preheat oven to 350℉
- Remove chilled dough and place into the hot oven. Bake 11-12 minutes, rotating halfway through. Do not over bake the cookies. It's actually okay if they are slightly under cooked, they will continue to bake as they cool.
- Sprinkle with flaky sea salt if you like the additional salt.
- Once completely cooled, move to an airtight container and store on the counter/fridge for 1 week or freezer for 3 months.
Nutrition
THANK YOU!
Thank you so much for trying this recipe, I hope you love these Brown Butter Pretzel Chocolate Chip Cookies as much as my family does. If you make this recipe, please share and tag me on Instagram or Facebook! And, please leave a comment or star rating below. I love to see everyone be successful in the journey to a healthier lifestyle with fresh milled flour! Don’t hesitate to contact me with any question, chances are we will both learn something from us working through it together!
Happy Baking!
Bailey Basics is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to amazon.com. I may earn a commission, with no additional cost to you, if you purchase through those links.
Bailey Basics is not a dietitian or nutritionist, and any nutritional information shared is an estimate. If calorie count and other nutritional values are important to you, we recommend running the ingredients through whichever online nutritional calculator you prefer. Calories can vary quite a bit.