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 Rachel! You mention in the ingredients that the starter should be fed, but in the notes it says it should be fed to 100% hydration. I’m about 2 weeks into my sourdough starter journey using your instructions, and would love to make these cookies but I’m not sure about the above instructions! I am about to discard some starter… can I refrigerate the discard but feed it at 100% hydration before putting in the fridge to use for the recipe tomorrow? Sorry if this is a silly question!
Hi Cat, 100% hydration just means you’ve been feeding the starter with an equal amount of flour and water, so it has the right consistency. You don’t need to feed the discard that you’re using. Hope this makes sense!
It does, thank you! I ended up making the dough last night, refrigerated it overnight and baked this morning and they turned out so well. Thank you for another great recipe!
I only have extra virgin coconut oil, will that work for this recipe?
Hi Carmen, yes it will! You will taste the coconut oil flavor though :)
as a long-time fan of Rachel’s regular chocolate chip cookie recipe, i have to 100% agree that there is something extra *special* about these! i make the dough in a big batch and freeze them in cookie scoop balls, and pop them onto a cookie sheet when i want some!
Prepping them like that is the BEST for cookies on demand! Thanks Andrea :)
Hi, I was wondering when you freeze them, do you bake them straight from the freezer or do you let them defrost a little bit? Thanks!
Hi Lena, I generally bake straight from the freezer, maybe thawing for 10-15 minutes if I have time. Hope this helps!
Thank you! They are delicious!
Rachel, The more I try your recipes, the more I am in love… These are amazing! The possibilities are endless with sourdough discard now. God knows I have enough of it… I have two starters I maintain. A sorghum one and a brown rice starter. The only substitution I made is I swapped the almond flour with hazelnut flower. Unfortunately, I am allergic to almonds. And they are my favorite….
Looking forward to trying the crackers next.
Haha, you’re just like me with the loads of sourdough discard Sandra!! So glad you’re loving these cookies, and happy they worked out well with hazelnut flour.
Any recommendations for getting coconut oil from solid to softened? Still cold here and we don’t have a microwave so can’t use that method. I find anytime I use the stovetop/oven it instantly melts and then I’m just working the problem in reverse. So excited to try this recipe though!
Hi Danielle, if you have a stand mixer, that can soften it up pretty quickly! Otherwise, a hairdryer works well to soften it a bit, and then just mush it around until the rest is softened as well.
Just amazing! I love the additional flavour profile from the sourdough. Will be a regular. Thank you x
So glad you’re loving them, Hannah!! Enjoy :D
Can I use 1 to 1 flour with this recipe instead of almond?
I don’t use 1 to 1 flours and they’re all different so you’d have to experiment at your own risk!
I made these today according to the instructions. Mine taste good, but spread out very flat. I’m at high altitude. Could that be the reason? Do you have high altitude adjustments?
Hi Sandy, I haven’t done much baking experimenting at high-altitude so I’m not sure if that would’ve affected it, but sometimes if you have a wetter starter with a higher hydration, the dough can be a bit wetter and spread more. Did the dough seem thinner than other cookie doughs you’ve made? I did just add a recipe note to add a bit more almond flour if that’s the case.
I used starter discard/opportunity that I had stored in the fridge over night. I had it in a glass bowl with a lid. Next day it had liquid on the top (hooch?) & smelled even more fermented/sour. Not fresh like before it went into the fridge. Is that normal? I went ahead & used it but wanted to make sure I was correct in putting a lid on it & that it was safe. The cookies turned out great but they have a slight sourdough aftertaste. Maybe because my discard was a day old?
Hi Elizabeth, yes the sourdough taste in the cookies would be because of the hooch. To avoid that alcoholic flavor, I’d drain off the hooch instead of stirring it in. It’s totally normal, and that often happens when your starter is hungry. And yes it’s totally safe! Just affects the flavor.
these are the best gluten free cookies I have ever made!! And they are egg free!! thank you!!
Yay!! Love to hear that :D
My daughter just said that these are the best gluten free chocolate chip cookies that she has ever had!!! That says everything in my opinion. She is 34 and has tried a lot of different recipes before. Thank you so, so much!!!
So happy to hear that, what a compliment! Thanks Susan.
I make these cookies regularly, and they are wonderful! Thanks so much for such a great, gluten-free recipe.
So glad you’re loving them, Shelley! :D
Any suggestions for an alternate to almond flour (no nuts for me right now). Have been working on my gf sourdough starter using your recipe and am excited to try some of your recipes. thanks in advance for any suggestions.
You can use oat flour instead!