Keto Pretzel Chocolate Chip Cookies

Annie Lampella @ Ketofocus

By Annie Lampella, Pharm.D.

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.

Keto pretzel chocolate chip cookies resting on a wire cooling rack with pretzels placed nearby for garnish.

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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Keto Pretzel Chocolate Chip Cookies

Prep 10m Cook 10m Total 20m 20 servings

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

1
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.

A rolling pin rests beside a zip-top bag of crushed pretzels used to add crunch to keto pretzel chocolate chip cookies.
Tip Don’t over-crush the pretzels into dust, you want small chunks mixed in so you actually get that salty crunch in every bite instead of the pretzels disappearing into the dough.
Ingredients for this step
  • 1/2 cup keto pretzels
2
Mix dry ingredients

In a medium bowl, pour in almond flour, coconut flour, baking powder, baking soda and salt. Stir to combine. Set aside.

A bowl of dry keto cookie ingredients is whisked together until evenly combined.
Ingredients for this step
  • 1 cup almond flour
  • 1/4 cup coconut flour
  • 1 teaspoon baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
3
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.

A hand mixer blends the keto cookie dough ingredients into a thick, creamy mixture.
Ingredients for this step
  • 1/2 cup unsalted butter, softened
  • 1/2 cup brown sugar substitute
  • 1 large egg
  • 1 teaspoon vanilla extract
4
Finish cookie dough

Slowly mix in dry ingredients until combined. Add chocolate chips and pretzels. Mix until combined.

Finished keto cookie dough with chocolate chips and crushed pretzels mixed throughout sits in a glass bowl.
Ingredients for this step
  • 1/4 cup sugar-free chocolate chips
5
Scoop & bake

  1. 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.

Baked cookies are arranged on a parchment-lined baking sheet.
Tip Taste test the cookie before adding salt on top. You may find they are salty enough for you without adding the salt on top.
Nutrition Per Serving 1 cookie
94 Calories
8.2g Fat
2.7g Protein
1.1g Net Carbs
7.6g Total Carbs
20 Servings
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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Keto Pretzel Chocolate Chip Cookies

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.

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A vertical stack of keto pretzel chocolate chip cookies on a cooling rack, showing their thick, soft texture.

Why I use both almond flour and coconut flour

I use a mix of almond flour and coconut flour in these cookies because they balance each other out. Almond flour brings that soft, buttery richness you want in a cookie, while a small amount of coconut flour absorbs extra moisture so the dough holds its shape. Without the coconut flour, I ended up with cookies that spread flat and came out greasy. With both, they bake up thick and tender every time.

How I store these (and freeze them for later)

If you somehow don’t eat these all the same day, you can store them in an airtight container on the counter for up to 3 days. I usually pop them in the fridge if I want them to last a little longer, about 5 to 7 days, and they firm up nicely while still staying soft in the center.

These cookies also freeze really well, just let them cool completely, then freeze in a single layer before transferring to a bag or container, and they’ll keep for a couple months.

You can also freeze the unbaked dough, just scoop it into balls first, freeze them solid on a baking sheet, then store in a freezer bag so you can bake a few cookies whenever the craving hits.

To reheat from frozen, I set them on the counter for about 15 minutes, then pop them in the oven at 300 degrees for 3-4 minutes. The oven matters here because the pretzel bits re-crisp in dry heat instead of going soft. The microwave works if you’re in a rush (10-15 seconds), but you lose that crunch on the edges.

About the Author
Annie Lampella, Pharm.D.

Annie Lampella, Pharm.D.

Annie is a Doctor of Pharmacy, mom, and the recipe creator behind KetoFocus. With a B.S. in Genetics from UC Davis, she has over 14 years of experience developing family-friendly keto recipes based on the science of human metabolism.

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