Last Updated on August 11, 2026 by Carrie Korem, FNTP
Sourdough chocolate chip cookies are a new favorite in our house! The cookies ferment in the fridge for 72 hours, which makes them a healthier alternative for dessert.
Ingredients for Sourdough Chocolate Chip Cookies
- Unsalted butter
- Organic cane sugar
- Organic brown sugar
- Bubbly sourdough starter
- Vanilla extract
- Egg
- Organic all-purpose flour
- Organic rolled oats
- baking powder
- Baking soda
- CCeltic sea salt
- Semisweet or dark chocolate chips (I use Enjoy Life)
Are sourdough cookies better for you than regular cookies?
Short answer: yes! And here’s why.
All grains contain something called phytic acid. It sounds harmless, but it actually blocks your body from absorbing important minerals like iron, copper and magnesium.
When you make the dough and let it sit in the fridge overnight, that resting time neutralizes the phytic acid. It also breaks down the carbs and gluten, making the cookies easier on your body to digest.
So the same cookie you love, just made a little smarter.
Are sourdough cookies easier to digest?
Here’s what’s actually happening when sourdough ferments slowly. The bacteria get to work breaking down the carbohydrates and gluten, and they also neutralize the phytic acid in the grain. That makes the cookies much easier for your body to digest.
There’s another perk too. Fermented sourdough contains healthy resistant starch, which means it won’t spike your blood sugar the way regular wheat cookies do.
To make sourdough cookies, you’ll need a sourdough starter. I personally used the Culture’s for Health Sourdough Starter and just followed the directions on the box. It’s easy to do, but you can also make the starter with just flour and water.
You can put different add ins such as pecans, flaked coconut, raisins, cranberries, etc. in your cookies to change up the flavors.
I hope you enjoy this recipe as much as I do!
PrintSourdough Chocolate Chip Cookies
- Prep Time: 72 hours
- Cook Time: 16 minutes
- Total Time: 72 hours 16 minutes
- Yield: Makes about 36 cookies
- Category: Dessert
- Method: Baking
- Cuisine: American
Ingredients
- 1 cup unsalted butter, room temperature
- 3/4 cup organic cane sugar
- 1/2 cup organic brown sugar
- 1/2 cup bubbly sourdough starter (see information about the starter in the post above)
- 2 teaspoons vanilla extract
- 1 large egg
- 2 cups organic all-purpose flour
- 1 cup organic rolled oats, ground fine in a food processor or blender
- 1/2 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp Celtic sea salt
- 1 1/2 cups semisweet or dark chocolate chips (I use Enjoy Life)
Instructions
- Place the butter and sugars in the bowl of a standing mixture and, using the beater attachment, mix on medium for 2 minutes. Scrape the sides of the bowl. Add the sourdough starter, vanilla and egg and mix on low until combined.
- In a separate bowl, combine the flour, oats, baking powder, baking soda and salt. With mixer on low, slowly add the dry ingredients to the wet. Then add chocolate chips and mix until just incorporated.
- Cover the bowl tightly and place in the refrigerator for 72 hours.
- To bake: Preheat the oven to 350ºF and adjust the rack to the middle position. Using a 2-inch cookie scoop, scoop the dough into balls and put on a baking sheet lined with parchment paper. Gently press on each cookie to flatten it a bit (so that it doesn’t have a dome on top). Bake for 14-16 minutes until just golden brown on the edges.
Photo Credit: Becky Winkler
Have you tried making these without grinding the oats? Would they bake the same? I really prefer the texture of oats just the way they are. 🙂
They won’t have the same texture. Grinding them makes a big difference!
I did it without grinding the oats as I do with most of my cookies and they are amazing!! Nice and chewy, the oat texture I love.
Great cookies!! Love this recipe!
I have made them multiple times without grinding the oats. They are delicious!
Because I prefer truly sourdough risen dough, I forego the baking powder and soda and double the salt, and these are STILL SO DELICIOUS!
I’m so glad you enjoyed them!
Hi, I would love to make your fermented sourdough chocolate cookies for my son. But his allergic to oats, based on a recent blood test. What other flour would you recommend to use instead? Thanks so much! Petra
I haven’t tested this recipe with substitutes so I’m not sure what would work well.
I Will try. One thing, i think that you can leave the final dough a few hours at room temperatur before continue the fermentation in the fridge to short the 72 hours . It’s like with Bread, i think. I Will tell you the results. Sorry for my english.
What if you have a jar of Unfed sourdough waste in the fridge from the week of starter feedings… will that be ok to use?!
You’d need to refresh it for a few days before using.
Could you use buckwheat flour instead and make your starter from buckwheat flour too? If it were me and I couldn’t eat oats I would substitute it with different nuts and crush them up to create an oatmeal texture like walnuts and macadamias. Give it a go and see what does and doesn’t work. Good luck!
Buckwheat won’t work the same as wheat flour, so I don’t recommend it.
I just made a batch and the dough is chilling in the fridge. Have you frozen extra dough or how long have you saved it in the fridge? I don’t know how the sourdough will react. But I’m gonna find out. Thanks for posting this fun recipe, can’t wait to try the cookies in 71 hours….
Can I ferment it for a shorter time – 48 hours instead of 72?
I recommend fermenting for 72 hours. I tested these every 24 hours and the 72 mark was where they had the best flavor. Plus, at this point, more of the sugars and gluten will have been broken down.
My daughter uses her insta-pot yogurt setting to proof her sourdough bread dough. I’ll bet it would work for these cookies, to decrease the ferment time.
A cold fermented is different than leaving it out at room temperature to ferment, so I don’t recommend trying to use an Insta-pot for this recipe.
Do you use gluten free oats or does it matter since you are fermenting the dough?
It doesn’t matter because you’re fermenting the dough.
Can I omit the rolled oats and use 3 cups flour instead?
That substitution won’t work for this recipe.
I asked the previous question about setting the dough to soften up a bit on the counter before baking. Knowing you probably wouldn’t get my message in time, I just went for it straight out of the fridge. It worked really well and these are really delicious and my stomach seems to approve as well as my teen whom I’m having to fight over them for😂
I’m so glad you enjoyed them!
They’re AMAZING!!!! I really can’t thank you enough! I haven’t had cookies in a very long time. My picky teen loves them as well!
I’m so glad you enjoyed them! 🙂
Hello! I just finished and am now waiting. Would they be okay if I waited longer than 72 hours?
Yes. As I mentioned in the post, I baked them also at 96 hours and they still tasted great!
Is this fermentation process creating alcohol since it’s sealed?
Not that I know of.
Even if it creates alcohol, it would evaporate during the baking time, I think.
Two years late to the punch here, but for anyone else who’s wondering, lacto fermenting (sauerkraut for example) and sourdough are different from the ferminting process which creates an alcohol byproduct. Different ingredients, yeasts, and bacteria are involved. So for those of us who abstain or have children to worry about, sourdough and lacto fermints are fine.
I have made this cookies and they are incredible! I don’t tolerate gluten very well so this recipe is great for me. I was wondering if I could freeze the cookies as the recipe makes a lot. Would it be better to freeze the baked cookies or half of the unbaked dough?
I’m so glad you enjoyed them! I froze a batch of dough balls and they worked great! One thing to note is that you’ll want to push down the frozen dough ball with your hand to flatten it a bit before baking so that it spreads when you bake it frozen.
I’m wondering about fermenting the baking soda. I thought baking soda was fast acting and therefore not able to make bake goods rise if not baked right away.
It works in this recipe!
Hi, so ready to make these but looking for some reasonable sugar substitute. Any tips please? I usually tend to use natural low carb sweeteners such as stevia or erythritol when baking. Thank you 🙂
I don’t test my recipes with substitutions, so I’m not sure what would work as a replacement.
I did use 1/2 sugar and 1/2 monk fruit for the total “sugar” measurement and they were still amazing. My family couldn’t tell and gobbled them up. I just fed my starter last night so I could make another batch! I can’t wait!!!
I’m so glad you enjoyed them!
I was a little skeptical of this recipe (never having let cookie dough sit for long!) but decided to give it a try. Due to circumstances over the weekend, I was unable to bake the cookies on Saturday at the 72 hour mark, and the dough sat in the fridge until this evening (Monday so 120+ hours) when my kids reminded me that it was in there. I baked some after school, they turned out beautifully and the kids loved them!! I’m glad I took the chance. Thanks so much for the great recipe!
I’m glad you enjoyed it!
I’d love to make these but as far as I can tell from googling it says eggs are safe only two days/48 hours in batter in the fridge. Is it something to do with the sourdough that makes it safe to keep this batter uncooked for a day more/72 hours? Not a criticism, just want to check that before I make them, they look awesome and sound healthier with the sourdough.
From my understanding, dough with eggs is safe for 3-5 days. Personally, I think it’s fine!
These sound incredible! I wanted to mail some to a friend who has gluten intolerance.
How many days will these hold up once baked?
I haven’t tested the exact amount of days, but they will hold up just like any other cookie…about 5 days or so.
would someone that thinks they have celiac issues be able to eat this better or those with stomach issues?
If some one thinks they have Celiac, I recommend they talk to their doctor.
How do you scoop them out? it’s hard like cement after 24hr! Is it supposed to sit outside for a few hours to soften?
With a spoon and a little arm strength. It shouldn’t be hard as cement. The dough is hard, but you should still be able to scoop it.
Next time I will make the dough I will shape it as a tube which makes it easy to slice the cookies and they will be in the shape for baking. Highly advisable! But they are by far the best cookies I’ve ever ever tried. I don’t like cookies at all. I only liked this cookies. Congrats on the wonderful recipe.
So glad you enjoyed them!
Great idea for next time as i had a hard time making them into balls from the fridge and your idea would make them flatter. Thank you.
What a great idea Cris!
ABSOLUTE PERFECTION!!!
Yay for sourdough cookies…These cookies are just so yummy! I can definitely see where the oat flour is beneficial to the recipe. I used half coconut sugar and half monk fruit/erythritol sweetener. Turned out tasty!! Thank you so much for sharing your recipe with us!
So glad you enjoyed them!
Just made the dough-not gonna lie-I licked the spoon and the bowl. So good! Can’t wait til Monday.
Hi. I’ve just prepared the dough as per the recipe, and now counting hours. However, I realise that ‘put in to ferment in the fridge’ allows fridge temp to be anywhere between 1-6 C… Please let me know, what should be the fridge temperature so that fermentation goes as it should? Thank you.
4C is a good temp for the fridge.
I don’t know if I can wait much longer to try these cookies. It’s been 36 hours….are they still good at that time? I just want a cookie, lol.
can i use sourdough discard or should i use fresh starter?
You need to use fresh, bubbly starter
Thanks for the recipe, these turned out great! I rolled the dough into logs and wrapped in wax paper before refrigerating for 72 hours. That allowed me to just slice off individual cookie sized pieces and put on the baking sheet.
I converted it to weights and tested it on my batch to confirm it turned out — here are the conversions (feel free to add them to your recipe for others if you’d like):
226g butter
189g sugar
129g brown sugar
120g starter
9g vanilla
1 egg
250g flour (I used half all-purpose, half white whole wheat)
100g oats, ground
3g baking powder
3g baking soda
3g salt
250g chocolate chips
I wasn’t thrilled with these – the cookies came out really dry. When I took the batter out of the fridge after 72 hours it was super hard, so I let it warm up to room temp but it didn’t soften much.
Also, I had to really flatten them on the baking sheet, or they didn’t spread at all when cooking.
I’ve made this recipe many times and they have never turned out dry, so I’m not sure what the issue was. Did you make any substitutions?
I have just taken the cookie dough out of the fridge and it seems really hard. I can hardly scoop it out. should I leave it a while at room temp?
Sorry just read all the comments and my question was answered. I have arthritis and find it very tough to scoop it out but will give it a go.
Update: I had somehow completely forgotten 1/4th of the batch of cookie dough in the back of the fridge for 3 weeks. I baked them as sort of a science experiment, wondering how sour they would have turned. I was surprised at how they still tasted just as delicious! In fact, they may have been even better!?! Tip: When I first refrigerated the dough, I had rolled it into logs so it was super easy to slice and bake a few at a time. Definitely will be making more to keep on hand in the fridge!
Can you substitute oat flour instead of grinding the oats? And if so would that still equate to 1 cup?
I haven’t tested the recipe with any substitutions so I’m not sure which ingredients would lend the exact same texture and flavor.
I made these and they spread much more than I thought they would. They tasted fine but were really very thin
I’ve tested these many times and haven’t had that issue. Did you make any substitutions?
Just want to clarify — for the oats, is it a measured cup of oats, then ground down to whatever that measurement would be? Or is it a measured cup of ground oats?
It’s as written. 1 cup of oats, then you grind them in the food processor.
These are delicious! I just made them for the first time. This recipe is a keeper….my husband and sons thoroughly enjoyed them. Great recipe!
I’m so glad you enjoyed them!
I don’t know what it is about these cookies that makes them taste so good, but they are one of the top chocolate chip cookies I’ve ever eaten. The dough just has so much flavor. Must be the starter!
Grinding the oats is definitely optional, we like the texture of whole oats in cookies and they turned out great.
I’m so glad you enjoyed them!
Hi, crazy question, wondering do you use the Enjoy life dark chips, or the semi-sweet mega chunks or mini chips –they don’t seem to have the regular size chips in semi-sweet……just wondering if you think the mini or mega size of the semi sweet affects the taste…making them more chocolatey or more sweet. thanks:)
I used the mini chips, but any of the Enjoy life that is semi-sweet would work!
Can these be made with any fermentation as with fermented yogurt? Can I use almond flour/coconut flour instead of organic flour?
I haven’t tested this recipe with any substitutions, so I don’t know what would lend the exact same flavor and texture.
This looks so good! What a great treat to make with kids!
Do you have to leave the baked cookies in the refrigerator or can they sit out and for how long?
Yes, the dough needs to fermented in the fridge.
Absolutely love these cookies. Mine for some reason don’t flatten as much but I don’t care because they’re still super good. I make a batch and freeze them and just bake them in the toaster oven whenever we want a few. I would be highly interested in more long-fermented cookie recipes if ever possible. (:
These cookies are great! I have been able to tolerate sourdough bread as I reintroduce gluten so I gave these cookies a try. They taste wonderful! But my gut did not like it. Should I ferment them longer?
I haven’t tested this with a longer fermentation, so I’m not sure
I haven’t tested this with a longer fermentation, so I’m not sure
Can you use coconut oil instead of butter or a combination of the two? Thank you!
I haven’t tested the recipe with substitutions, so I don’t know what would lend the exact same flavor and texture.
These cookies are absolutely delicious as well as super nutritiious. My children and grandchildren love them. Thank you.
These cookies deserve a prize!! The best chocolate chip cookies ever, I can’t even believe they are sourdough! The long fermentation in the fridge worked beautifully. The texture is spot on, truly the perfect cookie! My kids and husband were over the moon happy!! These are an absolute keeper! Thank you!!
I’m so glad you all enjoyed them! Thank you so much for the feedback!