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:

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:

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Gluten-Free Sourdough Chocolate Chip Cookies (Dairy-Free + Vegan)

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.8 from 31 reviews
  • Author: Bakerita | Rachel Conners
  • Prep Time: 10 minutes
  • Cook Time: 11 minutes
  • Total Time: 21 minutes
  • Yield: 12 cookies 1x
  • Category: Cookies
  • Method: Baking
  • Cuisine: Baking
  • Diet: Gluten Free


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.


  • ½ cup (100g) refined coconut oilsoftened, similar in texture to softened butter
  • ⅔ cup (96g) coconut sugar
  • 1 flax egg (see Notes) or regular eggroom 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 cups + 2 tablespoons (204g) blanched almond flour
  • 1 cup (6 ounces) chocolate chips
  • Flaky sea saltto sprinkle on top, optional


  1. Mix together the coconut oil and coconut sugar until smooth and lightened slightly in color. Add the flax egg (or regular egg), vanilla extract, and sourdough discard, and mix until smooth.
  2. Add the almond flour, salt, and baking soda to the wet ingredients. Mix until well incorporated. Fold in the chopped chocolate.
  3. Cover and refrigerate for at least an hour (or up to 48 hours).
  4. When you’re ready to bake, preheat the oven to 350ºF. Use a cookie scoop (using this size will give you 12 cookies, using this smaller size 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.
  5. Store leftover cookies in an airtight container at room temperature or in the refrigerator for up to 3 days.


For the flax egg: mix 1 tablespoon flax meal + 2.5 tablespoons water and let gel for 10 minutes before using

For the discard: don’t use discard that is from a super new starter – it should be smelling good and at least a week old. The starter does not need to be active, and should be fed with about 100% hydration.

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