Keto Pretzel Chocolate Chip Cookies
Published February 27, 2026
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If you love that sweet-salty thing, these keto pretzel chocolate chip cookies are about to be on repeat. They're thick, soft, and chewy with crunchy pretzel bits, melty chocolate, and just enough flaky salt on top to make you reach for one more (even though we both know it won't stop at one).
My oldest has a full-blown pretzel obsession, and I’m pretty sure he got it from me. And I got it from my mom. Salty, crunchy, snacky carbs have always been my weak spot, so when I discovered they actually make legit low-carb pretzels, I was way too excited. I keep a few bags stashed in the pantry at all times for snacking, road trips, and (let’s be real) stress eating. But the real lightbulb moment was realizing I could bake with them, which is how these cookies came to be.

I started with my go-to keto chocolate chip cookie base, the one I’ve made so many times I could probably do it half asleep. From there, it was just a matter of folding in crushed pretzels and letting that sweet-salty combo do its thing. The pretzels add that crunchy contrast that keto cookies are usually missing, and they somehow make the chocolate taste even better. I didn’t reinvent the wheel here. I just upgraded something I already know works.
The brand I use is Schoolyard Snacks pretzels (the classic twists). They hold their crunch in the dough better than any other brand I’ve tried, and the salt level is spot on. I’ve tested a couple of other brands that got soft and almost gummy once baked in, which defeats the whole purpose. If you can’t find Schoolyard, look for any pretzel that stays crunchy when you snap it in half. That snap is what you want surviving the oven.
From a recipe-testing standpoint, this one checked all my boxes. The cookies bake up thick, soft, and chewy in the middle with slightly crisp edges, and the pretzels hold their texture instead of disappearing into the dough. I baked six batches dialing in the pretzel crush size (too fine and they vanish, too chunky and they overpower the cookie) and settled on roughly pea-sized pieces. That’s the sweet spot for getting both crunch and salt in every bite.
No chill time needed, either. The almond flour and coconut flour combo holds the dough together right out of the bowl, so you can scoop and bake immediately. I actually prefer baking these straight away because the pretzels stay crunchier when they haven’t been sitting in wet dough for an hour.
One batch makes about 24 cookies, and they disappear fast around here. My family goes through them in about two days, so I usually double the recipe and freeze half the dough balls for later.
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Ingredients
1/2 cup keto pretzels
1 cup almond flour
1/4 cup coconut flour
1 teaspoon baking powder
1/2 teaspoon baking soda
1/2 teaspoon salt
1/2 cup unsalted butter, softened
1/2 cup brown sugar substitute
1 large egg
1 teaspoon vanilla extract
1/4 cup sugar-free chocolate chips
flaky sea salt for topping, optional
Step by Step Instructions
Step by Step Instructions
Preheat oven & crush pretzels
Preheat oven to 350 degrees F. Line a cookie sheet with parchment paper and set aside. Place pretzels in a large ziploc bag and crush into small pieces using a rolling pin. Set aside.
- 1/2 cup keto pretzels
Mix dry ingredients
In a medium bowl, pour in almond flour, coconut flour, baking powder, baking soda and salt. Stir to combine. Set aside.
- 1 cup almond flour
- 1/4 cup coconut flour
- 1 teaspoon baking powder
- 1/2 teaspoon baking soda
- 1/2 teaspoon salt
Combine wet ingredients
In a large bowl, drop in butter and brown sugar substitute. Cream together using an electric mixer until light and fluffy (about 2-3 minutes). Stir in egg and vanilla extract.
- 1/2 cup unsalted butter, softened
- 1/2 cup brown sugar substitute
- 1 large egg
- 1 teaspoon vanilla extract
Finish cookie dough
Slowly mix in dry ingredients until combined. Add chocolate chips and pretzels. Mix until combined.
- 1/4 cup sugar-free chocolate chips
Scoop & bake
- Using a 1 tablespoon cookie scoop, scoop cookies into balls and place 2 inches apart onto the lined baking sheet. Bake for 8-10 minutes until the edges are starting to get golden. Remove from the oven, sprinkle with flaky salt if desired and let cool completely.
Nutrition disclaimer
The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.
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Get My Macros + Recipes →Frequently Asked Questions
Can I use all almond flour and skip the coconut flour?
I've tried it, and I wouldn't recommend it. That small amount of coconut flour pulls its weight here, absorbing extra moisture and giving the cookies structure so they bake up thick instead of spreading flat. Without it, I ended up with fragile, greasy cookies that fell apart when I picked them up.
Why do my cookies look soft when they come out of the oven?
That's exactly what you want. I pull mine when the edges are just starting to turn golden, and they firm up as they cool. If you wait until they look fully done in the oven, they'll be dry and crumbly once they hit room temperature. I learned this the hard way with my first few batches of almond flour cookies.
Do I need to chill the dough before baking?
Nope. I bake these straight from the bowl every time. The almond flour and coconut flour combo holds the dough together without chilling, and I've found the pretzels actually stay crunchier when they haven't been sitting in wet dough. If your kitchen is really warm and the butter is getting soft, 10 minutes in the fridge won't hurt, but I've never needed it.
What brand of keto pretzels should I use?
I use Schoolyard Snacks classic twists. I've tested a few brands, and these hold their crunch the best once baked into the cookie. Some low-carb pretzels got soft and almost gummy in the oven, which defeats the whole purpose. Whatever brand you pick, snap one in half first. If it breaks clean with a good crunch, it'll work in these.
Can I swap the brown sugar substitute for a different sweetener?
I use Swerve brown or Besti brown because they cream well with butter and give that slight molasses-like warmth. If you switch to a liquid sweetener like monk fruit drops, the dough will be wetter and you'll need to adjust. I'd stick with a granulated brown sugar substitute for the best texture in these.
What are keto pretzels made of?
The ones I use (Schoolyard Snacks) are made with wheat protein isolate and fiber, which is how they keep the carb count low while still having that real pretzel crunch and snap. I'll be honest, I didn't look at the ingredients until my son asked. They taste like regular pretzels to me, and he can't tell the difference either. Most low-carb pretzel brands use some version of wheat protein or a cheese-based dough. If you're gluten-free on top of keto, check the label first because most of them do contain wheat-derived ingredients.
Can I make these with brown butter?
I haven't tried brown butter in this exact recipe yet, but I've used it in my other keto cookies and it adds this nutty, almost toffee-like warmth that I think would pair really well with the pretzel salt. If you go that route, melt the butter in a saucepan over medium heat until it turns golden and smells toasty, then let it cool to room temperature before creaming it with the sweetener. The cookies may spread a touch less and come out a bit crispier around the edges since browned butter has less moisture. I'm planning to try it on my next batch because that butterscotch-meets-pretzel-salt combo sounds worth testing.
How do I keep the pretzels crunchy after baking?
I had this problem with my first couple of batches until I figured out two things. First, crush size matters. If you pulverize them into dust, they absorb moisture from the dough and disappear. I settled on roughly pea-sized pieces after testing six batches, big enough to hold their structure through the oven. Second, skip the chill time. I know most cookie recipes tell you to refrigerate the dough, but the pretzels stay noticeably crunchier when they go straight from the bowl to the oven instead of soaking in wet dough. If you're storing baked cookies, the pretzels will soften slightly after a day or two on the counter. I pop them back in the oven at 300 degrees for 3-4 minutes and the crunch comes right back.
