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.




Hello! We love your blog any use several of your recipes with great success. This is the first one we’ve ever had to flop! They taste delicious but they flattened out completely when baking. Any suggestions on how to fix this?
Hi Ashley! So sorry to hear that – my guess is the starter was overhydrated which would make the cookies spread too much. Did the dough seem pretty soft when you went to bake?
I made the dough last night & baked them tonight. They are very good but your coconut flour chocolate chip cookies are my favorite go to cookie so I think I’m just not a huge fan of the almond flour. Do you think coconut flour could work here? If not I saw one reader used oat flour so I might try that next time. Thanks for the recipe!
Hi Izzy, you’d want to use 1/3 of the amount to use coconut flour because it’s such a different level of absorbency. I haven’t tried it, so experiment at your own risk!
Hi, made these, they are awesome!! Thanks for sharing receipe.
Running out of almond flour & before I’m able to get more wondering if I can sub 50/50 almond flour & gf flour blend?
FYI lemon cookies are in fridge waiting to bake, can’t wait!!
Hi Alice, yes that should be totally fine. Hope you’re loving the lemon cookies! :D
Delicious use of discard! Nice flavour, perfect level of sweetness. Made 15 large cookies. Beat oil and sugar at least 5 minutes. Add room temperature eggs one at a time, beating very well after each. Add all remaining ingredients and mix on low the very minimum required to barely mix. Refrigerate dough overnight. Using ice cream scoop, place dough balls on a parchment covered baking sheet. Don’t flatten and keep dough cold until it goes in the oven. Bake 12 minutes.
Thanks for sharing, Sherry! Glad you enjoyed it :)
I’m not going to lie these are AMAZING and so easy! I mixed everything together just before I went to bed, my egg wasn’t room temperature and I used butter instead of coconut oil because it was already soft.
I only had 2oz of chocolate chips left so I added 1oz of cacao nibs, 1oz of 100% dark chocolate and 2oz of chopped walnuts. I am always looking at ways to reduce sugar for my kids and this worked REALLY well so I’ll be doing it again next time!
I baked mine for 13 minutes at 150c in my fan assisted oven for any Brits reading this. I also let them cool for about five minutes on the baking sheet before moving them to a cooling rack.
They’re super soft, melt in your mouth delicious’ness, THANK YOU ❤️
So thrilled you’re loving them, Marsha!! Thanks so much for sharing your changes and feedback :)
Oh and can I add, if you warm one up and dollop some ice cream on its next level AMAZING! My kids had that tonight.
Sounds fantastic!!! :D
Looks like a wonderful idea! Any substitutions for the coconut sugar? Would maple syrup be a good alternative? if so, what ratio and would you omit the coconut oil as well? Thank you!
Hi Brie, I never recommend substituting a liquid sweetener for a granulated one because it messes up the texture! I recommend sticking to a granulated sweetener for this recipe.
I have made these cookies many times and they came out amazing ! However I double the batch this last time and the cookies came out flat? I can’t figure out what happen? Any suggestions to help them rise ?
Hi Raquel! Odd that it would happen when you doubled – any chance you mismeasured anything? Also, sometimes sourdough starter can be thinner than other times which can affect the texture. If you notice the dough being a little soft, you can always add extra almond flour to get the dough to the correct consistency.
Thank you so much for your input. I figured it out ! When you tap 2x on the top Of the recipes it doubles all the ingredients except the flour . I went back and really double checked myself Lol. When I figured it out and added more flour the cookies came out Perfect!! I are back in business!
Ooooh thanks for noticing that – let me figure out why that is and try to fix it!!
It doesn’t double the vanilla either. Is that on purpose or a fluke?
Sometimes the recipe card doesn’t work quite right for some reason – should be working now!
These are perfection! Will definitely make them my go-to gf sourdough discard use when I’m in the mood for a chocolate chip cookie. Or 6 ;) My husband and son loved them too! I got distracted and overbaked the first batch and they were a little dark but wonderfully crispy, perfect for dunking into unsweetened vanilla nut milk.
So glad you’re loving them! Nothing better than cookies & milk :)
Can suger be substituted with honey?
I wouldn’t recommend it, since it will throw off the liquid:dry ingredient ratio of this recipe!
Those cookies turned out amazing. This is I think the 4th time I try one of your recipes and each one was amazing! I m thankful I found your blog. Going gluten free and dairy free is a bit easier because of it :)