Gluten Free Sourdough Chocolate Chip Muffins are one of my favorite sourdough discard recipes to make.
These tender, fluffy muffins are made with a combination of gluten free sourdough discard and Greek yogurt for a subtle tang. Every bite contains a burst of rich, melty chocolate chips - it's basically like eating a chocolate chip cookie for breakfast.
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Looking for More Gluten Free Sourdough Discard Recipes?
These are some of my favorite gluten free sourdough discard recipes:
- Gluten Free Soft Pretzel Bites | Best Sourdough Discard Recipes
- Gluten Free Sourdough Sandwich Bread | Sourdough Discard Recipes
- Gluten Free Sourdough Pizza Crust - Best Sourdough Discard Recipes
- Gluten Free Sourdough Pie Crust - Sourdough Discard Recipes
- Sourdough Chocolate Chip Cookies | Gluten Free Sourdough Discard Recipes
- Gluten Free Sourdough Poptarts Recipe | Brown Sugar and Cinnamon
- Gluten Free Sourdough Poptarts | Homemade Strawberry Poptarts
- Gluten Free Sourdough Rolls | Best Fluffy Gluten Free Rolls Recipe
- Gluten Free Sourdough Pancakes | Sourdough Discard Recipes | Best Fluffy Pancakes
- Gluten Free Sourdough Banana Bread | Sourdough Discard Recipes

You will need gluten-free sourdough discard to make gluten free sourdough chocolate chip muffins, and preferably from a superfine brown rice flour 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.

Ingredients for Gluten Free Sourdough Chocolate Chip Muffins:
Dry Ingredients:
- High quality gluten free all purpose flour containing xanthan gum. I use Bob's Red Mill GF 1:1 (the blue bag).
- Light brown sugar
- Baking soda
- Baking powder
- Salt
- Semi-sweet chocolate chips. I love using Enjoy Life Semi-Sweet Chocolate Chips.

Wet Ingredients:
- Gluten free sourdough discard. Cold, straight from the fridge works well in this recipe.
- Milk
- Butter
- Greek yogurt
- Eggs
- Pure vanilla extract

How to Make Gluten Free Sourdough Chocolate Chip Muffins:
- Preheat the oven to 350 F. Prepare a silicone cupcake tray or grease/line a standard cupcake tray.
- In a large mixing bowl or bowl of a stand mixer, combine the dry ingredients: gluten free flour, brown sugar, baking soda, baking powder, and salt. Mix until combined.
- Add in the wet ingredients: gluten free sourdough discard, eggs, Greek yogurt, milk, melted butter, and vanilla extract. Beat until just combined.
- Fold in the chocolate chips.

- Allow the batter to rest for 10 minutes.
- Scoop the muffin batter into the prepared cupcake tray until the cups are ⅔ of the way full. I used a cookie scoop.

- Bake until lightly browned on top and a toothpick inserted in the center comes out clean, about 20-25 minutes. Since oven temperatures vary, keep an eye on your muffins as they bake so they don't overcook.

- Allow the muffins to cool in the pan for 5-10 minutes before placing onto a wire cooling rack. Allow the muffins to cool completely before storing.
- Enjoy!

Equipment
You only need basic kitchen tools to make Gluten Free Chocolate Chip Muffins. I recommend:
- A wire cooling rack is a must to prevent soggy bottoms
- I like to use a cookie scoop when scooping muffins into the tray
- A silicone cupcake tray or metal nonstick muffin tin. Sometimes I even use a jumbo muffin tin - just be sure to increase the bake time to 30-35 minutes or so.
- Reusable cupcake liners eliminate the need for paper cups
- Don't want to make a gluten-free 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 Muffins:
Store gluten free sourdough muffins in an airtight container at room temperature and enjoy within 2 to 3 days. You can also freeze these muffins. Once ready to eat, remove from the freezer and let sit at room temperature for 30 minutes. Warm in the microwave for 10-20 seconds to soften.

Notes
- Allow the batter to rest for 10 minutes before baking. This allows the rice flour to soak up some of the liquid, which can reduce grittiness in gluten free baked goods.
- If making jumbo muffins, you will need to increase the bake time to around 30-35 minutes.
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Gluten Free Sourdough Chocolate Chip Muffins | Sourdough Discard Recipes
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Equipment
- reusable silicone cupcake liners optional
Ingredients
Dry Ingredients:
- 1 ¾ cup (265g) high quality gluten free all purpose flour containing xanthan gum I used Bob's Red Mill GF 1:1 Baking Flour (the blue bag)
- ¾ cup (140g) light brown sugar
- 1 teaspoon (2g) baking powder
- ½ teaspoon (4g) baking soda
- 1 teaspoon (6g) salt
- 1 cup (180g) semi-sweet chocolate chips
Wet Ingredients:
- ½ cup (140g) gluten free sourdough discard cold from the fridge (or room temp)
- 1 cup (235g) plain Greek yogurt
- 2 (110g) large eggs
- 1 stick (100g) unsalted butter melted and slightly cooled
- 2 tablespoon (35g) milk
- 1 teaspoon (4g) pure vanilla extract
Instructions
- Preheat the oven to 350 F. Prepare a silicone cupcake tray or grease/line a standard cupcake tray.
- In a large mixing bowl or bowl of a stand mixer, combine the dry ingredients: gluten free flour, brown sugar, baking soda, baking powder, and salt. Mix until combined.
- Add in the wet ingredients: gluten free sourdough discard, eggs, Greek yogurt, milk, melted butter, and vanilla extract. Beat until just combined.
- Fold in the chocolate chips.
- Allow the batter to rest for 10 minutes.
- Scoop the muffin batter into the prepared cupcake tray until the cups are ⅔ of the way full. I used a cookie scoop.
- Bake until lightly browned on top and a toothpick inserted in the center comes out clean, about 20-25 minutes. Since oven temperatures vary, keep an eye on your muffins as they bake so they don't overcook.
- Allow the muffins to cool in the pan for 5-10 minutes before placing onto a wire cooling rack. Allow the muffins to cool completely before storing.
- Enjoy!
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