The best sourdough chocolate chip cookies may sound like a strange dessert, but this delicious cookie recipe has the perfect amount of sweetness and chocolatey goodness, balanced out with delicious sourdough. Don’t knock it until you try it! Active starter or sourdough discard will work for this recipe.

three sourdough chocolate chip cookies stacked up on a white plate with more cookies behind the plate on parchment paper

I know y’all probably think I have gone off my rocker, but hear me out.

I’m 100% baking my feelings over here. I’ve been working on so many delicious baked goods, mostly because I can, I have the time, and I’m 100% ok with eating my feelings being cooped up in my house.

While I want to bake all the things, there are a few considerations we have to keep in mind at our house.

My daughter is very sensitive to gluten (she isn’t celiac, though), but she can tolerate long-fermented sourdough products, like this skillet bread (just allow it to ferment for 12-24 hours before adding the remaining ingredients).

Gluten-free flour is pretty expensive, and sometimes a girl just wants regular glutinous flour, ok?

So I thought to myself, “hmmm… I wonder if I can long-ferment sourdough cookies to make them more digestible?”

That answer is yes! And they are sooo delicious.

A word to the wise: these are not quick cookies. Well, they totally can be quick if you don’t have a sensitivity to gluten. Just whip them up and bake them.

But to get the yummy sweetness and the perfect amount of sourness in these cookies, they need to ferment for 72 hours in the fridge. Yes. 72 hours.

I tried these by making them at 24, 48, and 72 hours. They truly developed the best sour taste at the 72 hour mark, and they were the most digestible.

Unfortunately, we found out how digestible they were the hard way.

My daughter tried them at 48 hours, and they gave her a belly ache, but after fermenting for 72 hours, she was perfectly fine. Odd, right?

sourdough cookies stacked up on a white plate with a blue and white stripped towel to the right

Why sourdough?

There is a sourdough revolution among us, and I love it.

Wheat can be difficult to digest for many people. When you make sourdough products, the fermentation breaks down the amount of gluten present (2) and contains pre-biotics and probiotics.

Both of these things can help make digesting wheat easier and more tolerable for many(3).

Also, wheat naturally contains phytic acid. Phytic acid is a anti-nutrient that decreases the body’s ability to absorb some of the nutrients present in wheat, like folate.

The fermentation process helps breaks down this phytic acid, increasing the nutrient profile.

Those who are sensitive to gluten may be able to tolerate long-fermented sourdough products. My daughter is one of those people.

If you find that you’re sensitive to gluten, you might be able to eat long-fermented sourdough without the bellyache that normally comes with eating gluten.

Since this recipe contains eggs and cannot sit out unrefrigerated, the fermentation process takes place in the refrigerator for a longer amount of time, since refrigeration slows the process.

overhead shot of sourdough cookies on a white plate and more on parchment paper to the right

Tips For Making This Recipe:

You can bake these sourdough chocolate chip cookies right away, or place them in a covered bowl and ferment in the refrigerator for 72 hours for the best flavor and digestibility.
I really like using mini chocolate chips. More chocolate is evenly distributed.
Cover pans with parchment paper for easy clean up.
New to sourdough? You can find my quick and dirty way to make a sourdough starter in 2 days, or you can find the traditional way over at my friend Lisa’s blog.
Active sourdough starter can be used, or turn these into sourdough discard cookies by using extra sourdough discard.

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Ingredients:

Brown sugar and cane sugar: Using these two types of sugar creates a really chewy and yummy cookie.

Butter : To soften butter quickly, pour hot water into a medium sized (large enough to cover the stick of butter) glass or ceramic cup or bowl. Allow the hot water to heat up the glass for a few minutes, pour out the water and cover the butter with the glass. Wait a few minutes and the butter should be softened

Egg

Vanilla extract: Homemade or store-bought

Sourdough starter – active or discard will work

All purpose flour

Salt – Brings out all the flavors and makes the cookies sweeter.

Leaveners: Baking powder and baking soda gives these cookies rise.

Chocolate chips – I love using mini chocolate chips

Tools you may need:

Stand mixer or hand mixer

Measuring cups and spoons

Silicon spatula

Stainless steel baking sheet

Why you will love this recipe:

Tasty: Delicious sweet and chewy, these chocolate chip cookies with sourdough starter are addicting.

Easier To Digest: Long ferment these cookies for easier digestion and more bioavailable nutrients.

Make ahead: Have a party or special occasion (or not) coming up? Make the dough days in advance and keep them in the fridge until you are ready to bake. Or make dough balls, place them on parchment paper, and freeze. Transfer into a freezer safe container to make cookies whenever you desire.

Great way to use excess starter: Have a lot of starter on your hands? These make great sourdough discard cookies. Never throw away discard again. Use them in a variety of dishes.

three chocolate chip cookies stacked up on a white square plate. More cookies on parchment paper in the background

How To Make Sourdough Chocolate Chip Cookies:

Feed your sourdough starter at least 4-12 hours before starting the cookies. You can also use discard. Either works.

butter, sugar, and brown sugar creamed together in a white ceramic mixing bowl on a stand mixer

In a stand mixer bowl, add brown sugar, sugar, and butter, and beat with the paddle attachment until pale in color.

sourdough starter, eggs, and vanilla being added to creamed sugar in a white ceramic mixing bowl on a stand mixer

Add in egg, vanilla, and sourdough starter. Mix until combined.

In a separate bowl, mix together dry ingredients.

dry ingredients being added to wet ingredients while a stand mixer is on low

While the mixer is on low, add in dry ingredients about 1/3 at a time until the dough forms. Don’t over mix, or you will have tough cookies.

chocolate chips being adding to sourdough cookie dough in a stand mixer

Mix in chocolate chips.

To make them right away: Spoon onto parchment lined baking sheet and bake at 350 degrees for about 15-20 minutes, or until they start to turn golden brown around the edges.

To long ferment: Place dough into a large bowl, add a lid, and place in the refrigerator for 72 hours. It can be as short as you like, but I found that 72 hours gave it the perfect amount of tanginess and the best digestibility.

Preheat oven to 350.

Spoon your fermented dough onto a parchment-lined baking sheet and bake at 350 degrees for about 15-20, minutes or until they start to turn golden brown around the edges.

Move to a cooling rack to cool. Enjoy.

sourdough chocolate chip cookies on parchment paper

How To Store:

Store in an airtight container for about 3 days. Do not refrigerate as it can make the cookies go stale faster.

You can also freeze already baked cookies in an air-tight container for up to 6 months. Lay in single layers and place a piece of parchment between layers.

Or make dough balls, place them on parchment paper lined baking dish in a single layer, and freeze. Transfer dough balls into a freezer safe container. Store up to 6 months. Bake one or a few cookies whenever you desire.

FAQ:

Why are my sourdough cookies flat?

Most likely, the leaveners are old and not very active or the oven is too hot.

What are the benefits of sourdough cookies?

If the sourdough cookies are long fermented then they will be easier to digest, have a lower gluten content, and the nutrients in the flour will be more easily absorbed by they body.

How long before you can bake with a sourdough starter?

If you are just starting your sourdough journey, you can easily start baking with the discard right away. It will not be able to make bread, but rather than tossing out the discard, use it in recipes that also call for a leavener like baking soda and baking powder like cookies, cakes, scones, muffins, etc.

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