These Gluten-Free Sourdough Chocolate Chip Cookies are going to be your new favorite way to use your gluten-free sourdough discard! They’re dairy-free, vegan, and some of the best cookies you’ll ever have.

Have you been on the gluten-free sourdough bread journey with me, lately? If you have, you’re probably being left with a lot of gluten-free sourdough discard, and you’re probably wondering what you should make with all of it…especially if you’ve had your fill of cinnamon sugar sourdough discard crackers.
Well, come along for this journey with me, because I’ve got your new favorite way to use sourdough discard right here: Gluten-Free Sourdough Chocolate Chip Cookies.

What is sourdough discard?
When you’re building a sourdough starter (gluten-free or regular), you discard half of the starter with each feeding to keep it at a manageable size. That part of the starter that we take out is referred to as “sourdough discard.” There is nothing wrong with it – we just want to keep our starter manageable and not have to feed it a bag of flour every time.
But, if you hate wasting food like me, you’ll never want to actually discard your sourdough discard. I usually scoop mine into a jar, and bake another treat that day using it! If you’re not baking with your discard that day, you can keep it in the refrigerator, or even the freezer, until you’re ready to use it. But, why throw something away, why you can use it to make more delicious goodies?!

How can I use my gluten-free sourdough discard?
There are a lot of ways to use up your sourdough discard. I’ve seen tons of recipes using it in a variety of baked goods, crackers, etc. but most don’t consider gluten-free sourdough discard! So, I’ve started developing my own gluten-free sourdough discard recipes and found a few I go back to regularly. Some favorites include:
- Gluten-Free Cinnamon Sugar Sourdough Discard Crackers
- Sourdough Pancakes (GF) from Vanilla & Bean
- Gluten-Free Sourdough Discard Crackers with Herbs from Homestead & Chill
And of course, my newest favorite, these Gluten-Free Sourdough Discard Chocolate Chip Cookies!

What ingredients do I need?
This recipe is pretty similar to my favorite famous Paleo Chocolate Chip Cookies, but adjusted slightly to add the sourdough discard, which makes the cookies a little softer and gives them a little extra *something something*. Here’s what you need to make them:
- Coconut Oil: you can substitute butter or vegan butter, if preferred.
- Coconut Sugar: my preferred sweetener – adds an amazing caramelly flavor.
- Flax Egg: you can also use a regular egg if you’re not vegan.
- Vanilla Extract: for flavor :D
- Gluten-Free Sourdough Discard: I’ve used both my brown rice starter and my sorghum starter, just make sure it’s at 100% hydration (or close to it) – it should be a thick paste.
- Almond Flour: gives a fabulous texture!
- Baking Soda: for a little lift.
- Salt: always a baking must!
- Chocolate Chips: I love using coconut sugar-sweetened chips here to keep refined sugar-free.

Let’s make Gluten-Free Sourdough Discard Chocolate Chip Cookies!
This recipe follows the pretty standard steps for cookie-making!
To start, you’ll combine the coconut oil and coconut sugar and mix until they’re well combined and lightened in color.
Then, you’ll mix in the flax egg, vanilla extract, and your gluten-free sourdough discard.
Next, stir in the almond flour, baking soda, and salt. The dough should be thick, but may seem a little softer than a traditional cookie dough. If you find it seems very soft (which can happen with a thinner starter), add in more almond flour until you get a soft but firm cookie dough consistency. Note that it will firm up slightly in the refrigerator.
Finally, stir in your chocolate chips, and the hardest part: place in the refrigerator for at least an hour. This is a must – it allows the sourdough discard to combine with the rest of the ingredients and allows the dough to thicken up and develop flavor.
You can let your dough sit anywhere from an hour to up to 48 hours! The longer you let the dough sit, the stronger the sourdough flavor will be.
When you’re ready to bake, preheat the oven and scoop and bake as usual!

How do they taste?
Right after tasting, my dad said “what did you do to these? They’re the best cookies you’ve ever made.” Considering how many cookies I make, that’s a big compliment!
The sourdough discard doesn’t add a lot of sourdough flavor to the cookies/ To be quite honest, I was a little nervous before tasting them – but they don’t taste sour at all. The sourdough discard adds a little extra flavor you can’t quite put your finger on, but I think it makes these cookies even better. My dad obviously agrees.
About these Gluten-Free Sourdough Discard Chocolate Chip Cookies…
- They’ve got soft, gooey centers
- Crispy edges
- Loaded with chocolate chips
- Easy to make
- Perfect to make-ahead
- Store great
- Perfect use for your gluten-free sourdough discard

Other gluten-free sourdough discard recipes:
- Gluten-Free Cinnamon Sugar Sourdough Discard Crackers
- The Best Gluten-Free Sourdough Pizza Crust
- Chocolate Chip Gluten-Free Sourdough Scones
- Gluten-Free Sourdough Discard Crackers

Gluten-Free Sourdough Chocolate Chip Cookies (Dairy-Free + Vegan)
Ingredients
- ½ cup (100g) refined coconut oil, softened, similar in texture to softened butter
- ⅔ cup (96g) coconut sugar
- 1 flax egg, see Notes or regular egg, room temperature
- ½ cup (125g) mature gluten-free sourdough starter, unfed (see Notes)
- 1 teaspoon pure vanilla extract
- ½ teaspoon baking soda
- ½ teaspoon sea salt
- 2 1/4 cups (220g) blanched almond flour, if your cookies seem "wet", add a bit more flour to get to a thicker consistency
- 1 cup (6 oz) chocolate chips
- Flaky sea salt, to sprinkle on top, optional
Instructions
- Mix together the coconut oil and coconut sugar until smooth and lightened slightly in color. Add the flax egg (or regular egg), vanilla, and sourdough discard, and mix until smooth.½ cup (100g) refined coconut oil, ⅔ cup (96g) coconut sugar, 1 flax egg, 1 teaspoon pure vanilla extract, ½ cup (125g) mature gluten-free sourdough starter
- Add the almond flour, salt, and baking soda to the wet ingredients. Mix until well incorporated. Fold in the chopped chocolate.½ teaspoon baking soda, ½ teaspoon sea salt, 2 1/4 cups (220g) blanched almond flour, 1 cup (6 oz) chocolate chips
- Cover and refrigerate for at least an hour (or up to 48 hours).
- When you’re ready to bake, preheat the oven to 350ºF. Use a cookie scoop (using a bigger scoop will give you 12 cookies, using a small scoop will give you about 20) to form cookies and place on a parchment-lined baking sheet; press down slightly. Sprinkle with flaky sea salt if desired. Bake for about 10 or until just beginning to turn golden brown around the edges.Flaky sea salt
- Store leftover cookies in an airtight container at room temperature or in the refrigerator for up to 3 days.




Hi where do I buy sourdough discard. ? I’m confused.
Hi Karen, did you read the beginning of the post? This recipe is meant to use sourdough discard, which comes from your sourdough starter. You can use my original chocolate chip cookie recipe if you’re not making sourdough.
Hi
I have a sourdougj starter which is not gluten free.can I make using same recipee
Hi Kavita, I haven’t tested with a gluten starter so I can’t say with confidence either way!
I’m rather disappointed you said that. Anyone celiac must avoid gluten at any cost. Calling your recipe GF when using a gluten based starter is then misleading. It is possible to make a GF starter and we do this to avoid gluten.
Hi Suz, I’m not sure what you mean? All of my sourdough recipes are gluten-free and use my recipe for gluten-free sourdough starter. I would never call a recipe gluten-free and then use a gluten product in it. If others want to use a gluten-based starter in this recipe because they don’t have celiac, that is up to them, but that is not how the recipe is written.
Sorry Rachel…I don’t know where my head was. What I wrote is so not what you do.
I just did this actually! I have a non gf sourdough starter but predominantly eat gluten free. So, I mixed this up using 2 cups bobs red mill all purpose flour and the non gf starter. The rest followed the recipe. It turned out! The cookies it made are very soft and not too sweet.
Amazing! As soon as I saw this recipe was live, I ran to the kitchen to bake up a batch and boy are they amazing! As always, thanks for another incredible recipe!
So happy you’re loving them – so good, right?!
Tried them for the first time and they were great. Also kiddo approved!
So glad you’re loving them, April!!
These cookies are amazing!! Perfect texture and flavor, WOW! Super easy, all in one bowl which I love. I used an egg and my sourdough starter is brown rice/sorghum and you’re right, it’s not sour at all it’s totally delicious!! I love that I have a great use for my discard now yay!!
So glad you’re loving them, Vanessa!!! :)
Seriously!!!! The BEST…and sooooo easy to make!
Definitely worth it to prepare the night before and bake in the morning! I brought them to my job site and people flipped out… Especially after hearing they were vegan and gluten-free and refined sugar free. So much flavor! So grateful …I can’t wait to make my second batch {in a few minutes :) . Mahalo, Rachel!!!!!
Woohooo!!! So glad they were a hit, Lala! One of my new favorites, for sure.
I would love to try the recipe, but I can not tolerate almonds. Do you have an alternative I could use?
Hi Anette, oat flour or another nut or seed flour (like hazelnut, cashew, or sunflower seed) would work well here!
Thank you so much for your help. I used oat flour and the cookies turned out amazing!
So glad to hear that!!
Tigernut flour works SO well as a sub for almond flour! :)
I agree – thanks for sharing this!! Tigernut flour can be harder to find sometimes, but definitely works super well as an almond flour replacement.
These sound Great. I do not have almond flour, but I have ground almonds. I’m wondering if I could substitute that. I did that in another recipe and it worked okay.
I’m also wondering if you have any thoughts on using a combination of ground almonds and brown rice flour. (I can’t use oats, or I’d try them.)
Thank you. :-)
Hi Kathryn, that should be okay, but if they’re a little gritty, that’s why! I haven’t tested this recipe with brown rice flour, so unfortunately can’t say how well it would work, but you’re welcome to experiment!
Hi – I just found your blog and I’m really excited by all your recipes, they look great! I just made this using the weights and 2 cups of almond flour weighed only ~60 g, so I kept adding flour and the batter got dryer and dryer. Eventually I stopped before it got too sandy/dry but I haven’t used the full 204 g. What is the consistency of this cookie dough meant to be like?
Hi Emma, it sounds like your scale is off because there is no way 2 cups of almond flour would only weigh 60g – that’s the equivalent of less than 2/3 of a cup! It should be the consistency of regular cookie dough, if anything a bit thinner than usual because of the sourdough starter. Use your instincts and if it seems too dry, it usually is! :) I would make sure your scale is well-calibrated (a good test is one cup of water should be 8 oz.) before using it again!
These are delicious, soft and chewy, and even my picky and typically unwilling to try vegan/GF or sourdough thing kiddos absolutely love them! They were easy to make as well. This recipe will be a permanent entry into my recipe book! Thank you Rachel!
Woohoo, love to hear that Amanda!! Thank you so much :D
Soft, chewy, not too sweet easy chocolate chip recipe. The discard does not make it taste sour. Delicious.
So glad you’re loving it! Thanks for the feedback, Justina!