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.




These are the best chocolate chip cookies! I made them for the holidays and no one could believe they are gluten free. Great job Rachel!!!
So glad you loved them :D
I followed the recipe exactly and didn’t have a great result. Maybe because I don’t like the oily taste of coconut oil. The texture was somewhat grainy too. Something was awry. The one thing I did different was make the cookies a bit smaller, I got 24 out of the recipe.
Hi Barb, sometimes the starter has an impact on something like that – if you’ve been using a coarser brown rice flour for your starter, that texture can translate to the cookies. You can use refined coconut oil to reduce any coconut flavor you don’t like, or use a vegan or regular butter if you prefer.
The cookies were kind of crumbly. They were ok, but I’ll stick with my other recipes for chocolate chip cookies.
Sorry that they disappointed you, Jef! Any chance your starter was particularly thick/dry? What flour starter do you have? For this recipe, the starter can have an effect on the outcome of the cookies and if yours was on the drier side, than it definitely could’ve absorbed extra moisture from the cookies – I’ve always found these cookies to be particularly soft!
My starter was 100% hydration and made with brown rice flour. The cookies were soft, but fell apart pretty easily.
Hi Jef, was the starter on the thin or thick side? Were they cooled completely on the baking sheet?
A little on the thin side since the starter was not a peak, but not watery thin. And I did let them cool on the sheet.
The taste of these was amazing! I used avocado oil because I didn’t have coconut. They were very soft and fell apart after baking for 13-14 mins. Any way to make them more sturdy? Or should I increase baking time a bit? Thank you for sharing!
So glad you enjoyed them, Jazmin! Coconut oil firms up when at room temp, similar to butter, and avocado oil doesn’t – that difference can definitely make cookies softer which make have been the issue. A thinner, runnier starter (which usually means it has more water) can also make the dough softer. If your starter seems thin, you may want to add more flour to get it to a thick, pasty consistency before using. That should help make a thicker dough that will hold up better. You can also just add a bit more flour. Hope this helps!!
Didn’t have coco oil subbed butter. Didn’t have coco sugar – subbed brown and castor sugar. Figured I would be ok… until I realized I had used UNblanched almond flour. The he teen said they tasted like a major bakery house product and husband insisted on taking some with him with his coffee in his he morning. I’m sooo glad I don’t have to eat them all. Extremely forgiving recipe. Thank you!
So glad you enjoyed them, Mhairi! One of my favorite recipes :)
Great simple recipe that can be done by hand in one bowl! Also, for me it was very forgiving; I had No coconut oil nor sugar so I subbed melted butter and half brown sugar half white sugar. After making them I realized that my almond flour was unblanched – no worries they were still great. My teen didn’t notice the starter. I’m definitely making these again. FYI I needed to bake this. I’m I for about 15 minutes. Thank you!
Are there other flour options, besides almond? I’m not vegan; based on your expertise, do you believe I can substitute the coconut oil for softened butter 1:1?
Butter is a perfect sub for the coconut oil if you’re not vegan. You can use other flours, almond is the only one I’ve tested though. Is there a certain flour you were hoping to use?
Wonderful cookies!
Glad you’re loving them Helen!
I’ve been GF for over 20 years but am new to GF sourdough and this was my first discard recipe. These cookies are fantastic! I only used 1/2c of chocolate chips but added 1/2c of chopped pecans and used an egg. So soft and chewy. I ended up with 30 cookies and baked them for 15 minutes.
Thanks for the delicious recipe, I’ll definitely be making these again.
So glad you’re loving them, Monika! I appreciate the review :)
These cookies look lovely, but your multiply ratio seems to be wrong on the first two items please could you correct it for us thanks
Hi Anne, what ingredients are you seeing multiply incorrectly? I just tested it out and the multiply feature functioned correctly for me.