Gluten Free Sourdough Chocolate Chip Cookies are a perfect way to use up some extra discard. These cookies have a soft-baked and fluffy interior with a chewy, golden brown exterior and a generous disbursement of chocolate chips. For a slight sourdough tang, use discard up to two weeks old.

As an Amazon Associate, I earn from qualifying purchases. This post contains affiliate links for products I use and love. You can read my full disclosure here. All thoughts and opinions expressed are my own. Thank you for supporting Wonders of Cooking so that I can continue to provide you with free gluten-free recipes.
You will need gluten-free sourdough starter discard to make these cookies, and preferably from a superfine brown rice or sorghum flour starter.
If you don't have a gluten-free sourdough starter, you will first need to make one and can find out how with my guide on How to Make a Gluten Free Sourdough Starter.
Looking for more Gluten Free Sourdough recipes?
- Gluten Free Sourdough Banana Bread | Sourdough Discard Recipes
- Gluten Free Sourdough Bread Recipe | Dutch Oven Method
- Gluten Free Sourdough Discard Crackers | Best Gluten Free Cracker Recipe
- Gluten Free Sourdough Pancakes | Sourdough Discard Recipes | Best Fluffy Pancakes
- Gluten Free Sourdough Pizza Crust - Best Sourdough Discard Recipes
- Gluten Free Sourdough Pie Crust - Sourdough Discard Recipes
- Gluten Free Sourdough Sandwich Bread | Sourdough Discard Recipes
- Gluten Free Sourdough Poptarts Recipe | Brown Sugar and Cinnamon
- Gluten Free Sourdough Chocolate Chip Muffins | Sourdough Discard Recipes

What is sourdough discard?
Sourdough discard is the portion of starter removed before feeding. Instead of throwing it away, it’s typically stored in a jar in the refrigerator. This discard is considered inactive because the wild yeast and bacteria have already used up the flour and water, and no fresh food has been added.
Since it no longer provides leavening, sourdough discard works best in recipes that don’t rely on yeast to rise, such as brownies, cookies, banana bread, other quick breads, and crackers.

What are the benefits of eating gluten free sourdough?
Sourdough is well known for its potential health benefits. Although it contains gut-friendly lactobacillus, these probiotics are destroyed during baking, so sourdough does not provide live probiotic benefits. Still, sourdough is a fermented food, meaning the bacteria and wild yeast living within the starter predigest the starches in the flour, making the food easier to digest. This may also help support more stable blood sugar levels. For these reasons, sourdough is often considered gentler on the gut.
For those living with Celiac disease (like myself), diets often rely heavily on rice-based products. Gluten-free sourdough offers a way to incorporate a wider variety of grains, such as sorghum, millet, and buckwheat.

Ingredients for Gluten Free Sourdough Chocolate Chip Cookies:
- Gluten-free sourdough discard (the unfed portion removed from the starter, up to two weeks old)
- High quality gluten-free all purpose flour containing xanthan gum. I used Bob's Red Mill GF 1:1 Baking Flour (the blue bag).
- Unsalted butter. You can also swap for dairy-free butter, such as Earth Balance.
- Granulated sugar
- Light brown sugar
- Baking soda
- Baking powder
- Eggs
- Pure vanilla extract
- Salt
- Semi-sweet chocolate chips. You can also use half chopped nuts and half chocolate chips.

How to Make Gluten Free Sourdough Chocolate Chip Cookies:
- Prepare a large cookie sheet (or two small cookie sheets) by greasing with cooking spray, a sheet of parchment paper, or a silicone baking mat. Set aside.
- In a large mixing bowl or the bowl of a stand mixer fitted with a paddle attachment, cream together the butter, granulated sugar, and brown sugar until light and fluffy.
- Add in gluten-free sourdough discard, eggs, and vanilla extract. Mix until well-distributed.
- In a medium-sized mixing bowl, add the GF flour, baking powder, baking soda, and salt. Whisk until combined.
- Add the dry ingredients to the wet in intervals, mixing well and scraping down the sides of the bowl. Be careful to not over-mix.

- Fold/stir in the chocolate chips.
- Scoop the cookie dough (about 2 tablespoons per cookie) and roll into balls. Space them 2-inches apart on a cookie sheet. Tip: If the cookie sheet doesn't fit in the fridge, place the balls on a platter.

- Chill the cookie balls in the refrigerator for 30 minutes to an hour. Chilling the dough helps prevent the cookies from spreading when baked, and it gives the batter a chance to rest which can reduce any grittiness from gluten-free flours.
- About halfway through the chilling time, preheat the oven to 375 F.

- Bake the cookies for 10-12 minutes, or until the middles are set and the edges are golden brown. Allow to cool five minutes before removing to a wire cooling rack. Repeat with any remaining batches.
- Enjoy!

Equipment
Making Gluten Free Sourdough Chocolate Chip Cookies requires no special equipment. As long as you have basic mixing bowls and a cookie sheet, you'll be good to go!
- Parchment paper or a silicone baking mat is preferred for easier clean-up.
- I also recommend using a 2 tablespoon cookie scoop because it's so much faster and makes the perfect shaped cookies.
- A wire cookie rack helps cookies cool quickly and prevent soggy/greasy bottoms.
Don't want to make a starter from scratch? This Sourdough Starter Culture packet gives you a head start with a dehydrated gluten-free sourdough starter culture and directions to follow to maintain it for years to come. I love this website because there's also cheesemaking, yogurt, kombucha, and fermented vegetable kits.
(Use the code WONDERS15X on Cultures For Health's website to get 15% off!) The GF starter is also available for purchase on Amazon here.

How to Store Gluten Free Sourdough Chocolate Chip Cookies:
Store these cookies in an airtight container at room temperature and enjoy within 3 to 5 days. Tip: You can also freeze baked cookies and thaw them once ready to eat.
Want to get ahead on Christmas baking or keep an emergency stash of gluten-free cookies on hand? You can easily prep these ahead by freezing the unbaked dough balls.
How to Bake Frozen Cookie Dough Balls:
- Preheat the oven to 350 F.
- Line a baking sheet with parchment paper.
- Place the frozen cookie dough balls on the sheet, spacing two inches apart from each other and the sides of the pan.(No need to thaw—bake straight from frozen.)
- Add 1 to 3 extra minutes to the baking time. Bake this frozen peanut butter cookie dough for 12 to 16 minutes instead of 10 to 12.
- Bake until the edges are set and lightly golden but the centers still look slightly soft.
- Cool on the baking sheet for 5 minutes before transferring to a rack.

Notes on Gluten Free Sourdough Chocolate Chip Cookies:
- For more of that classic sourdough tang, you can ferment the dough (chill) these cookies between 12 to 24 hours.
- Semi-sweet chocolate is best. Use either chocolate chips or chunks, your choice. Additionally, you can replace half of the chocolate with chopped nuts or dried fruit.

Have you tried these Gluten Free Sourdough Chocolate Chip Cookies? Leave a 5-Star rating below!
You can also join my Facebook group, Gluten Free Sourdough Baking Recipes and Advice, to share recipes, post photos, and get advice in live time. Currently we have 6000 members and growing!

Sourdough Chocolate Chip Cookies | Gluten Free Sourdough Discard Recipes
Your rating helps support the making of more tested, delicious gluten-free recipes.
Equipment
- 2 tablespoon cookie scoop optional
- silicone baking mats optional
Ingredients
- 2 sticks unsalted butter (1 cup) *can replace with non-dairy butter such as Earth Balance
- 1 cup light brown sugar
- ¾ cup granulated sugar
- ¾ cup gluten-free sourdough discard (the unfed portion removed from the starter, up to two weeks old)
- 2 large eggs
- 2 teaspoon pure vanilla extract
- 2 ¾ cups high-quality gluten-free all purpose flour containing xanthan gum I used Bob's Red Mill GF 1:1 Baking Flour (the blue bag)
- 1 teaspoon baking soda
- ½ teaspoon baking powder
- 1 teaspoon salt
- 2 cups semi-sweet chocolate chips
Instructions
- Prepare a large cookie sheet (or two smaller sheets) by greasing with cooking spray or lining with parchment paper or a silicone baking mat. Set aside.
- In a large bowl, or in a stand mixer fitted with the paddle attachment, cream the butter and sugars together until light and fluffy.2 sticks unsalted butter (1 cup), 1 cup light brown sugar, ¾ cup granulated sugar
- Add the gluten-free sourdough discard, eggs, and vanilla extract, and mix until well combined.¾ cup gluten-free sourdough discard, 2 large eggs, 2 teaspoon pure vanilla extract
- In a medium bowl, whisk the dry ingredients until combined.2 ¾ cups high-quality gluten-free all purpose flour containing xanthan gum, 1 teaspoon baking soda, ½ teaspoon baking powder, 1 teaspoon salt
- Add the dry ingredients to the wet ingredients in intervals, mixing just until combined and scraping down the sides of the bowl as needed. Avoid overmixing.
- Fold in the chocolate chips.2 cups semi-sweet chocolate chips
- Scoop the dough (about 2 tablespoons per cookie) and roll into balls. Place them 2 inches apart on a cookie sheet. Tip: If the sheet won’t fit in the fridge, place the dough balls on a platter instead.
- Chill the dough balls in the refrigerator for 30 minutes to 1 hour. This helps prevent spreading during baking and allows the gluten-free flours to hydrate, reducing any gritty texture.
- About halfway through the chilling time, preheat the oven to 375 F.
- Bake the cookies for 10 to 12 minutes, until the centers are mostly set and the edges are golden. Let them cool for 5 minutes on the sheet before transferring to a wire rack. Repeat with remaining batches.
- Enjoy!
Notes
- For more of that classic sourdough tang, you can ferment the dough (chill) between 12 to 24 hours.
- Semi-sweet chocolate is best. Use either chocolate chips or chunks, your choice. Additionally, you can replace half of the chocolate with chopped nuts.
How to Bake Frozen Cookie Dough Balls:
- Preheat the oven to 350 F.
- Line a baking sheet with parchment paper.
- Place the frozen cookie dough balls on the sheet, spacing two inches apart from each other and the sides of the pan.(No need to thaw—bake straight from frozen.)
- Add 1 to 3 extra minutes to the baking time. Bake this frozen peanut butter cookie dough for 12 to 16 minutes instead of 10 to 12.
- Bake until the edges are set and lightly golden but the centers still look slightly soft.
- Cool on the baking sheet for 5 minutes before transferring to a rack.





Leave a Reply