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.




What does “fed with about 100% hydration.” mean?
It means the starter should be fed with equal amounts of starter/water/flour.
Hello, I really love your recipes. I’ve been making your GF sourdough bread weekly for months. And I loved the chocolate chip scones using discard. I just made these and they all ran together to form a giant cookie. I didn’t see anyone else with that issue so I’m not sure what I did wrong. I used virgin coconut oil and an egg, everything else was just as written in the recipe. I also refrigerated the dough for an hour. Thanks.
Danielle
Hi Danielle, so sorry you had an issue! Usually with discard recipes, my first question is about the discard, since that’s the biggest variable – was it super runny? If it was, the extra moisture from the discard may have been the problem, but you likely would have noticed that with a super runny/wet dough. Did it seem like a thick cookie dough or too soft?
These are awful. They fall apart and have no structure. I am a microbakery and bake cookies all the time. They crumble terribly and the coconut flavor is overpowering to the chocolate. They’re grain as hell too. Super unpleasant. What a waste.
Sorry you had trouble, Amber. These have been super successful for me and most folks who have made them. Did you use refined coconut oil, as recommended? It doesn’t have any coconut flavor, and if you used virgin, that would be the cause of the coconut flavor. It’s also super important to use finely blanched almond flour, not almond meal, or the results will be crumbly. Sourdough starter can also be a big variable here – if you use a coarse flour or the starter is super runny, it will impact the texture of the cookie.
Hey!
I made these last night, and my husband and I loved them! However, this morning when I opened the Tupperware that stored them in, I noticed that they all felt soggy. They were a totally different texture than what they were last night. Any ideas of what may have happened?
Hi Kaela, were they warm at all (even a little bit) when you stored them? If they were, the extra steam would cause them to soften significantly. Putting them in the fridge will likely help them firm up a bit!
Any idea of the nutrition information for these (rough estimate of kcals)? I know small vs large scoop will be different.
Awesome recipe! Definitely learned that any more than 12 minutes at 350 is too long (I burnt the bottoms the first time I made them). 12 made light golden bottoms and slightly soft cookies, which were amazing! This is my new favorite recipe.
Hi Erin, just added nutritional info based on the recipe making 18 cookies, which is about a standard small scoop. It would be a bit more for a medium sized cookie scoop. Hope this helps!
Thank you so much! These cookies are a big win in our household.
I love everything about these cookies. They taste amazing. The only issue I’m having is that they are breaking apart easily. Is there something I can do to prevent this from happening?
Hi Bianca, these cookies can be a little on the softer side especially if your sourdough starter is a little thinner. To make them a little bit more firm you can add some extra almond flour or a tablespoon or two of coconut flour, which can help them firm up.
These were great! My only question… they were very soft and break easily. I wouldn’t call them crumbly just very soft. Any tips for next time?
Hi Shelly, did your starter seem thin? This is usually the cause of these cookies being soft! A little extra flour can help firm up the cookies. It should be a thick cookie dough texture.
Thank you for your reply. No, my starter was more like a thicker pancake batter. I did use the scale to measure out the coconut oil and I did put them in the refrigerator. I thought maybe the coconut oil made them extra soft?!
These cookies are absolutely amazing. My whole family tore them up had no idea they were gluten free at all. I used my own oat flour after another person commented using it also. Oat flour worked very well for this one!
So glad they were a hit, Ly. Thanks for the feedback and star rating!
These are delicious. I followed to recipe using Psyllium husks. I added about a handful of chopped pecans. Will definitely be using this recipe to use up my discard. Thanks!
So glad you’re loving them, Stephanie. Thanks for the feedback!
I substituted applesauce for the oil, and it worked!
These are absolutely delicious!
My husband said they’re the most cookie-like cookie we’ve had since going vegan.
So thrilled your fam is loving them, Ami! Thanks for the star review and feedback.