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Sourdough Discard Chocolate Chip Cookies

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These sourdough discard chocolate chip cookies can be made with einkorn flour for optimal digestion and nutrient count. They have a chewy texture, are soft, gooey, and melt-in-your mouth GOOD. No kidding, these are my favorite chocolate chip cookies IN THE WORLD.

It’s kind of ironic that I’m writing this post right now, because my husband and I are actually on a sugar fast. (It won’t last forever. Telling myself that now.) But ever since I developed this particular sourdough chocolate chip cookie recipe, I’ve been on the edge of my seat wanting to share it with you. Because they really are the best cookies ever.

I wanted to create a sourdough cookie recipe that paired well with einkorn flour, because, well, it’s kind of my favorite. And it’s more easily digestible. But don’t worry–you can also make these chewy chocolate chip cookies with regular all-purpose flour, if that’s what you have on hand!

sourdough chocolate chip cookies on white plate with glass of milk

This post contains affiliate links, which means I may make a small commission at no extra cost to you. See my full disclosure here.

Is einkorn flour healthy?

Pretty much everything I bake uses either einkorn or sourdough–or both. Whenever my family and I eat unfermented all purpose flour, we notice that our tummies feel a little more unsettled due to its gluten and phytic acid content.

Einkorn wheat is an ancient grain, and I’m a big fan. Einkorn is often easier for people with gluten sensitivities to tolerate, because it’s genetic makeup forms a different kind of gluten. It’s also higher in protein, antioxidants, vitamins, and essential fatty acids compared to modern wheat.

Tools you may need to make sourdough chocolate chip cookies:

Here are some of my favorite kitchen items that I personally use to make these cookies (and a ton of other sourdough baked goods).

sourdough discard chocolate chip cookies on white plate

Ingredients list for sourdough discard chocolate chip cookies:

  • Butter: Makes these cookies deliciously chewy and gooey. I usually use salted butter because that’s what I already have on hand, and I like the added flavor. But unsalted butter can be used just as well. It should be softened before you start.
  • Sourdough starter (can be in active or discard stage):  Gives these cookies a tang and rich depth of flavor. If you’re using active sourdough starter, the sour flavor will be lessened.
  • Vanilla extract: I like to make my own with vodka and fresh vanilla beans, but any extract will work!
  • Eggs: Bonus points if they’re fresh from the hen.
  • Einkorn or all purpose flour: Be sure to check the recipe card for exact measurements, depending on which flour you’ll be using.
  • Organic cane sugar (or suitable substitute): If I am going to use sugar, it’s going to be non-GMO.
  • Brown sugar (or suitable substitute): I often just make my own brown sugar because I don’t always have it on hand. Dark or light will work, just choose what suits your tastes!
  • Kosher salt: Using kosher salt or another kind of flaky salt really sets off the flavor of these cookies.
  • Baking soda: Self-explanatory.
  • Chocolate chips: Use the highest quality you can find for the best results!
sourdough einkorn chocolate chip cookies stacked on plate with glass of milk being poured

Healthy sourdough discard cookies

This is a sourdough discard recipe that doesn’t require any extra fermentation. Meaning, these sourdough cookies can be whipped up quickly this afternoon! Although they aren’t long fermented, these chewy cookies are a great way to enjoy a dessert that’s healthier than most, especially if made with einkorn wheat.

Here are a few substitution ideas to make these sourdough discard cookies even healthier:

  • Substitute coconut sugar for the brown and/or white sugar to lower the glycemic index
  •  I recently discovered this monk fruit sweetener by Whole Earth that measures 1:1 (equal parts) for sugar. It would make another great sugar substitute option.
  • Use Lily’s chocolate chips in place of regular chocolate chips. You could also do extra dark chocolate chips instead of traditional semi-sweet.
  • Try using softened coconut oil instead of butter if you’re trying to stay dairy-free.

Many of these substitute ingredients, as well as my favorite einkorn flour can be found at Thrive Market for a great discounted price! If you live in an area that lacks access to healthy groceries, Thrive is an excellent online membership site where you can shop and get them shipped to your door, while also staying on budget. Sign up here and get an extra 30% off your first order plus a FREE gift!

bag of einkorn flour next to large stainless steel mixing bowl

Tips and Notes for Sourdough Chocolate Chip Cookies

This recipe makes 3-4 dozen chocolate chip cookies, but before I go into how to make them, know that you can half the recipe if needed. We have a fairly large family, and these cookies are still delicious after being sealed in an airtight container for a couple of days. Therefore, we don’t mind having extras! But you don’t have to.

Other Notes

  • You can pre-portion into cookie dough balls, store in an airtight container for up to a week, take them out and bake any time you want fresh cookies.
  • If you are using active starter for this recipe, the flavor will be less sour. They may also have a bit more of a cake-like texture.
  • Bake for 10 minutes if you like your cookies slightly underbaked, 12 minutes or longer if you like them more firm and golden brown.
  • cookie scoop will ensure your cookies stay at a consistently round size.
sourdough chocolate chip cookies on white plate with glass of milk in background

How To Make Sourdough Discard Chocolate Chip Cookies

Add 2 sticks of softened butter and 1/2 cup each of of brown and regular cane sugar to a large mixing bowl or the bowl of a stand mixer. Beat well.

butter and sugar about to be creamed together in stand mixer

Add 1 cup of sourdough starter discard, 2 eggs, and 1 tbsp of vanilla extract to the bowl. Beat until smooth.

wet ingredients for sourdough chocolate chip cookies in bowl of stand mixer

In a separate smaller mixing bowl (or you can just do this in the same bowl on top of the wet ingredients, as is my custom. I talk about it more in my recipes for sourdough brownies and sourdough banana bread), mix flour of choice, 1 teaspoon of baking soda, and 1 teaspoon of kosher salt. Combine the dry ingredients with the wet ingredients by using the paddle attachment of a stand mixer, or by hand with a wooden spoon. Finally, fold in the chocolate chips.

Once the dough is all mixed, refrigerate it for 30 minutes to 1 hour before baking. You technically could skip this step. But, I find the dough is much easier to handle when it’s not room temperature, and the cookies don’t spread quite as much.

When it’s almost time to bake, preheat the oven to 350°F. Drop dough by rounded tablespoonfuls on parchment or silpat covered baking sheets. Place in the preheated oven and bake for 10-12 minutes.

Remove and let cool on the cookie sheet for 5-10 minutes before transferring to a wire rack. If the cookies make it past this stage, you’re doing better than we usually do, ha! 

einkorn sourdough chocolate chip cookie with melted chocolate

Once completely cooled, you can store the cookies in an airtight container for up to 3 days.

I hope you enjoy these soft, chewy sourdough chocolate chip cookies! If you did, remember to comment and rate below the recipe card!

​Can’t get enough sourdough?

Me either. I have a FREE ebook called Sourdough Discard Favorites, and it’s full of easy sourdough discard recipes your family will love. To get it, just enter your email below:

You can also grab the recipe card for my signature rustic sourdough bread right here!

5 from 3 votes

Sourdough Discard Chocolate Chip Cookies

Use up sourdough discard with these chewy, gooey chocolate chip cookies that can also be made with protein-packed einkorn flour.
Print Recipe
Prep Time:10 minutes
Cook Time:15 minutes
Total Time:25 minutes


  • 1 cup butter softened
  • 1/2 cup organic cane sugar
  • 1/2 cup organic brown sugar
  • 1 cup sourdough starter
  • 1 tbsp vanilla extract
  • 2 eggs
  • 2 1/2 cups einkorn flour or 2 cups all purpose flour
  • 1 tsp baking soda
  • 1 tsp kosher salt
  • 2 cups chocolate chips


  • Add butter and sugars to a large mixing bowl or the bowl of a stand mixer. Beat well.
  • Add sourdough starter, eggs, and vanilla extract to the bowl. Beat until smooth.
  • In a separate smaller mixing bowl, mix together einkorn or all purpose flour, baking soda, and kosher salt.
  • Add dry ingredients to wet and mix using paddle attachment on a stand mixer, hand mixer, or with a wooden spoon. Fold in the chocolate chips.
  • Refrigerate dough for 30 minutes to 1 hour and preheat oven to 350°F.
  • Drop dough by rounded tablespoonfuls on parchment or silpat covered baking sheets. Place in preheated oven and bake for 10-12 minutes.
  • Remove and let cool on the cookie sheet for 5-10 minutes before transferring to a wire rack.
Course: Dessert
Cuisine: Sourdough
Keyword: cookies, sourdough
Servings: 3.5 dozen
Calories: 155kcal

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Recipe Rating


  1. 5 stars
    Excellent recipe! I’m always looking for new ways to use my discarded sourdough starter. Your cookies are so nice and fluffy!

  2. 5 stars
    Swapped butter for coconut oil, and only went with 1/2 cup of chocolate chips. We also baked in an air fryer for 9 minutes at 350° for nine minutes, and then air fried for one minute at 400°. Rotated the outside edges of the cookies in before air frying. They turned out with a crisp, outer edge, and super soft and fluffy on the inside. Still have a bunch of discard, so may try again with only coconut sugar and see what happens.

    Thanks for sharing the recipe!