Big Chocolate Chip pretzel Cookies Recipe

My BIG chocolate chip pretzel cookies recipe is all about that salty and sweet perfect combination! We’re taking my healthy whole wheat dark chocolate chip cookies, and adding crunchy pretzels into them. A fun and delicious twist you’ll want over and over again!

Chocolate chip pretzel cookies recipe

Made with less sugar and whole wheat flour, these delicious cookies have a healthy twist!

But don’t worry, there’s still a little butter and chocolate in them (hello super good cookie!). The salty pretzels take them over the top!

The recipe makes 6 big chewy cookies and it’s quickly become one of our family’s favorite cookie recipes.

You can also use a small cookie scoop and opt for crushed pretzels instead for some delicious mini cookies! Any Cookie Monster would approve.

Can you freeze these cookies?

Yes! 

You can freeze cooked cookies, simply cool them, and then freeze them individually on a parchment paper-lined baking sheet. I suggest making a double batch if you plan to freeze them!

Once frozen solid, transfer to a freezer bag and they will keep for up to 3 months.

You can also freeze the cookie dough. Mix the dough, then scoop out the cookies. Freeze the individual unbaked cookies on a parchment paper-lined baking sheet. 

Once frozen solid, transfer to a freezer bag and the cookie dough will keep for up to 3 months.

To bake your frozen cookie dough, no need to defrost it. 

Take the unbaked cookie dough out of the freezer, and follow the baking instructions below, adding 2-3 more minutes to the bake time.

What you need for this pretzel chocolate chip cookies recipe

• whole wheat pastry flour
• baking soda
• sea salt
• room temperature unsalted butter
• natural cane sugar
• egg
• pure vanilla extract
• dark chocolate chips
• pretzels

How to make our favorite cookies

Scroll down to view the recipe card below for the full ingredients list, nutrition facts, and step-by-step instructions.

1. Preheat the oven to 350 degrees F and set aside a cookie sheet.
2. In a large bowl whisk together the softened butter, sugar, egg, and vanilla.
3. In the same bowl, add the flour, baking soda, and sea salt.
4. Stir the dry ingredients in with the wet ingredients, along with the chocolate chips and pretzels until just combined.
5. Using a spoon or large cookie scoop, scoop 6 cookie balls onto the baking sheet.
6. Bake for 15-17 minutes until golden brown and the bottoms are crispy. Allow cooling on a wire rack.

Watch me make chocolate chip pretzel cookies

The full how to video can be watched below, or on my YouTube channel!

What to serve with classic chocolate chip cookies

Cookies and milk (or homemade almond milk!) are a go-to in our house!

We also love to make healthy chocolate banana ice cream and then crumble a cookie over top of it. Makes it extra special!

Another fun way to use these cookies is in my protein cookie dough. Replace the chocolate chips with broken-up cookies for healthy protein cookies and cream cookie dough – YUM!

How to store

Any leftover cookies should be cooled thoroughly before placing them in an airtight container for storage.

Enjoy at room temperature, or slightly re-warm them to get that soft and melted chocolate center.

Substitutions

Below you’ll find a list of substitutions that will work well in this dark chocolate pretzel cookies recipe. 

If you try something different out, please leave a comment below letting us all know how it turned out!

Whole wheat pastry flour – All-purpose flour, whole wheat flour, and an all-purpose gluten-free flour mix will work as substitutes here.

Butter – Unsalted sweet cream butter can be replaced with salted butter, however, you’ll want to use unsalted pretzels if your butter is salted. Ghee (clarified butter) is another great option. For less buttery cookies, try coconut oil in place of the butter.

Natural cane sugar – White sugar, date sugar, coconut sugar, and light brown sugar will all work in place of natural cane sugar.

Dark chocolate chips – Dark chocolate chunks, milk chocolate chips, semi-sweet chocolate chips, peanut butter chips, or mini chocolate chips all work in place of the dark chocolate option. You can also chop up your favorite bar of chocolate to use here too!

Pretzels – This salty treat is thanks to the pretzels, and you can use any shape of pretzel you’d like here – pretzel sticks, pretzel twists, or even pretzel balls (chopped up).

More recipes your sweet tooth will love

• Vegan oatmeal chocolate chip cookies
• Chickpea cookie recipe
• Chocolate oatmeal almond flour cookies
• Chewy orange almond butter oat cookies

If you try this homemade chocolate chip cookie recipe, I’d love it if you left a star rating and comment below letting me know how it turned out!

XO

Heather

Originally published May 2012. Updated December 2022.