The best sourdough chocolate chip cookies are soft, chewy, and packed with chocolate chunks. Keep this recipe in your back pocket for a quick dessert or a long-fermented treat.

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‘Tis the season for cookies. The house is gleaming with Christmas cheer. Our Victorian Farmhouse Christmas Tour showcases greenery along the staircase and pops of red running through each room.
While we occasionally make typical Christmas sugar cookies, I still prefer a soft, buttery, chocolate chip cookie.
I highly suggest allowing this recipe to ferment overnight if you can. This fermentation time makes the cookies healthier, while also adding a delicious and subtle tang that pairs perfectly with the sweetness.
If you have never tried a sourdough dessert, I think you will be pleasantly surprised.
Now If you don’t have the time for long-fermentation, you can also make these up and bake them right away. They’re incredibly delicious either way.
In this case, I’ll often swap the all-purpose flour out for einkorn flour. My motto has always been that if you can’t sour it, use einkorn, such as in these Toasted Coconut Cookies.
This means that if you don’t have the time for fermentation, which aids in digestibility, just switch over to einkorn flour for its great nutritional qualities.
It’s a whole wheat flour that is more easily digested than typically processed flour, and it adds depth with its nutty flavor.
Sourdough baking has been a passion of mine for over ten years now. It has so many health benefits!
One of the greatest is that fermenting decreases the phytic acid to make the nutrients more bio-available and the grain more digestible.
I’ve spent a lot of time learning how to convert recipes to sourdough, because creating more nourishing foods is so important in our family. Hence, chewy sourdough chocolate chip cookies.
Why you will love this recipe:

Use up your discard: This is a great recipe for using up extra discard and adding tasty sourdough flavor to a classic cookie.
Chewy and delicious: These cookies are mouthwatering, packed with butter and chocolate, with a delightfully chewy texture and sourdough tang.
Versatile: You can make this dough up to three days in advance and store it in the fridge to have freshly baked cookies at a moment’s notice (all while the dough ferments).
You can use milk chocolate, semisweet, or dark chocolate chips, add chopped nuts, or top with flaky salt to make them just how you like them!
Ingredients

Butter: When baking, I prefer to use unsalted butter. This allows you to control the amount of salt added to the cookies.
Sourdough starter: Active starter or sourdough starter discard can be used for this recipe.
Vanilla extract: Vanilla adds such a rich, warm flavor. I use my homemade vanilla extract.
Chocolate chips: In my opinion, chocolate chunks are far superior to chocolate chips. Both will work, I just like the chunks better.
A full ingredient list with exact amounts can be found in the recipe card below.
Tools you may need:
Grain mill (optional)
Stand mixer or hand mixer

How To Make Sourdough Chocolate Chip Cookies

Step 1: In a stand mixer with a paddle attachment, cream together butter, white sugar, and brown sugar until light and fluffy. Add eggs, sourdough discard, and vanilla. Mix again until light and fluffy.

Step 2: In a separate bowl, mix flour, baking soda, baking powder and salt.

Step 3: Slowly add dry ingredients to wet ingredients. Scrape down the sides and mix well. Once combined, add chocolate chips and mix well. If you would like to long-ferment the dough, cover the bowl with a tight lid (i.e. plastic wrap, lid, beeswax wrap) and place it into the fridge. For best digestion, I recommend three days.

Step 4: Roll cookies into a ball using three tablespoons of dough per cookie. Place them two inches apart on a parchment-lined baking sheet. Chill in the refrigerator for at least an hour, or up to 3 days for a longer fermentation. I think the best results for texture and taste are achieved when they sit in the fridge for 12-24 hours!

Step 5: Preheat the oven to 375°F. Once preheated, remove the cookies from the fridge and bake for 10-12 minutes. The edges should start to turn a golden brown.

Step 6: Remove from the oven and immediately transfer to a wire rack to cool.

Storage
Room Temperature: Store in an airtight container at room temperature for up to a week.
Freezing cookie dough: Make the dough (long-fermented or the quick version) and scoop out cookie dough balls onto a parchment-lined baking sheet.
Freeze on the sheet. Once frozen, transfer to an air-tight container or freezer-safe bag. When you’re ready to use them, bake according to the directions above. They may take slightly longer to bake from frozen. Cookie dough will last three months in the freezer.
Freezing Baked Cookies: Bake and allow to cool completely. Place the baking sheets (with the cookies and parchment paper in place) in the freezer for a few hours.
Once frozen, place the cookies in an airtight container. You can put parchment paper between layers if desired. Frozen cookies will last three months in the freezer. Allow to thaw at room temperature. Bake for just a few minutes for a nice warm cookie.
Tips for Making Sourdough Cookies
- If you are new to sourdough, I have a post all about how to make a sourdough starter from scratch.
- Make this recipe and bake right away, or ferment the dough for up to three days for the most health benefits and easier digestion. The instructions on how to make them long-fermented versus the faster version vary slightly.
- I highly suggest using chocolate chunks. While chocolate chips are wonderful, something is extra amazing about chocolate chunks (especially the ones from Trader Joe’s – they are the best!).
- I would recommend using a cookie scoop. It is the most reliable way to get your cookies a consistent size and evenly baked.
- Be careful not to overbake or overmix the dough or your cookies won’t be as soft and tender.
Recipe FAQ
Sourdough is a good option because of the fermented grains in the discard, and a long-fermented dough will be more easily digested and utilized. They still contain sugar and fats, so moderation is key, but fermentation does reduce the sugar and add flavor.
Either will work. Since you don’t need to rise this recipe like you would a sourdough bread, you can use either.
No. You can follow the non-fermented version. You won’t reap the benefits from the ferment, but if you have no issues digesting grains, then whip them up and bake them right away.
The secret is in the baking time. A shorter bake time will give you a softer cookie, whereas a longer bake time will give you a fluffier, more cake-like cookie.
Yes! Absolutely. This is how I recommend long-fermenting cookies.
Yes, you can put the whole bowl in the fridge to ferment! Then just shape and bake.
More Sourdough Recipes from the Farmhouse
- Sourdough Thumbprint Cookies with Discard
- Sourdough Snickerdoodle Cookies
- Sourdough Oatmeal Cookies
- Chewy Sourdough Gingerbread Cookies
- Sourdough Peanut Butter Cookies
- Sourdough Sugar Cookies
- Easy Sourdough Christmas Cookie Recipes
- Sourdough Pumpkin Cookies
If you try this recipe and love it, I would appreciate if you could come back, commented on the post, and give it 5 stars! Thanks.
















Always turn out delicious!
If freezing the dough, should you let it sit in the fridge prior to rolling out balls and freezing?
Freezing cookie dough: Make the dough (long-fermented or the quick version) and scoop out cookie dough balls onto a parchment-lined baking sheet.
Freeze on the sheet. Once frozen, transfer to an air-tight container or freezer-safe bag. When you’re ready to use them, bake according to the directions above. They may take slightly longer to bake from frozen. Cookie dough will last three months in the freezer.
I have made these cookies for the last two weeks and they get rave reviews from my customers. I’ve tweaked the recipe to include an extra cup of chocolate chips and make sure they are assorted with milk, semi sweet and dark chocolates. Bake them up in 4 ounce balls. Package and sell while they are still warm. Best chocolate chip cookie I’ve ever made. My customers line up for them!!!
Hi I love these cookies but I always have a problem with them spreading out. Even if I freeze or have in the fridge for over 12 hours. They taste so good but I can not figure out what is causing them to flatten.
Thank you
First thing to check is …are you using the same flour as I used in the recipe? Next try using gram measures if you aren’t already…as that is a more precise way to measure. Lastly here are some other things to look at..Even if you chill the dough for a long time, the following factors can cause them to flatten:
• Excessively Hot Ovens: If the oven temperature is too high, the fat inside the cookie melts and spreads out rapidly before the flour and structure have a chance to set properly.
• Stale Leaveners: Old or expired baking soda or baking powder loses its strength. Without that fresh chemical reaction, the cookies won’t get the necessary lift to puff up, causing them to bake flat instead.
• Butter and Room Temperature: When creaming the dough, recipes on the blog call for unsalted butter softened to room temperature so it can fluff up properly with the sugars. If your kitchen is very warm or the butter gets too soft before mixing, it won’t trap enough air during creaming, leading to less volume and a flatter bake.
Hi I love these cookies but I always have a problem with them speaking bout. Even if I freeze or have in the fridge for over 12 hours. They taste so good but I can not figure out what is causing them to flatten.
Thank you
First are you using the same type of flour I did in the recipe? Next try measuring in grams if you haven’t already as that is the most accurate measure. Finally, even if you chill the dough for a long time, the following factors can cause them to flatten:
• Excessively Hot Ovens: If the oven temperature is too high, the fat inside the cookie melts and spreads out rapidly before the flour and structure have a chance to set properly.
• Stale Leaveners: Old or expired baking soda or baking powder loses its strength. Without that fresh chemical reaction, the cookies won’t get the necessary lift to puff up, causing them to bake flat instead.
• Butter and Room Temperature: When creaming the dough, recipes on the blog call for unsalted butter softened to room temperature so it can fluff up properly with the sugars. If your kitchen is very warm or the butter gets too soft before mixing, it won’t trap enough air during creaming, leading to less volume and a flatter bake.
These are delicious cookies. I make a batch of dough, scoop them onto a lined baking sheet, and freeze until firm. Then they go into a freezer zip bag and are ready to bake any time we need cookies.
I’ve probably made this recipe over 25 times now. I will forever keep coming back to it!!! Must always have these cookies on deck!
I baked a bunch of these for my family, and they are absolutely obsessed with them. I haven’t cookies this good in a long time. I will be adding this to my recipe book for future baking 🙂
Delicious! Everyone loved them
This makes the best cookies! These have become a family favorite, thank you for sharing.