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    You are here: Home / Breakfast / Gluten Free Sourdough Chocolate Chip Muffins | Sourdough Discard Recipes

    Gluten Free Sourdough Chocolate Chip Muffins | Sourdough Discard Recipes

    March 15, 2024 By madison 4 Comments

    Jump to Recipe Print Recipe

    Gluten Free Sourdough Chocolate Chip Muffins are one of my favorite sourdough discard recipes to make.

    They’re tender and fluffy, made with a mix of gluten-free sourdough discard and Greek yogurt for a hint of tang. Each bite is filled with rich, melty chocolate chips—it’s basically like having a chocolate chip cookie for breakfast.

    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

    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.

    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

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    • Looking for More Gluten Free Sourdough Discard Recipes?
    • Ingredients for Gluten Free Sourdough Chocolate Chip Muffins:
        • Dry Ingredients:
        • Wet Ingredients:
    • How to Make Gluten Free Sourdough Chocolate Chip Muffins:
    • Equipment
    • How to Store Gluten Free Sourdough Chocolate Chip Muffins:
    • Notes
    • Did you Make These Gluten Free Sourdough Chocolate Chip Muffins? Leave a 5-Star Rating Below!
    • Gluten Free Sourdough Chocolate Chip Muffins | Sourdough Discard Recipes
      • Equipment
      • Ingredients
        • Dry Ingredients:
        • Wet Ingredients:
      • Instructions
      • Notes

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    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

    You'll need gluten-free sourdough discard to make gluten free sourdough chocolate chip muffins, preferably from a superfine brown rice or sorghum flour starter.

    If you don't have a gluten-free sourdough starter, you'll first need to make one. Find out how with my guide: 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.
    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

    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.
    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog
    • 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.
    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog
    • 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!
    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

    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.
    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

    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.

    Gluten Free Sourdough Chocolate Chip Muffins by Wonders of Cooking food blog

    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.

    Did you Make These Gluten Free Sourdough Chocolate Chip Muffins? Leave a 5-Star Rating Below!

    Gluten Free Sourdough Chocolate Chip Muffins

    Gluten Free Sourdough Chocolate Chip Muffins | Sourdough Discard Recipes

    5 from 3 votes

    Your rating helps support the making of more tested, delicious gluten-free recipes.

    Prep Time: 15 minutes mins
    Cook Time: 25 minutes mins
    Total Time: 40 minutes mins
    Yield: 12 muffins
    Tender, fluffy muffins 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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    Author: Madison @ Wonders of Cooking

    Equipment

    • wire cooling rack
    • cookie scoop
    • silicone cupcake tray or
    • nonstick metal muffin tin or
    • jumbo muffin tin
    • 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. Mix until combined.
      1 ¾ cup (265g) high quality gluten free all purpose flour containing xanthan gum, ¾ cup (140g) light brown sugar, 1 teaspoon (2g) baking powder, ½ teaspoon (4g) baking soda, 1 teaspoon (6g) salt
    • Add the wet ingredients to the dry, and beat until just combined.
      ½ cup (140g) gluten free sourdough discard, 1 cup (235g) plain Greek yogurt, 2 (110g) large eggs, 1 stick (100g) unsalted butter, 2 tablespoon (35g) milk, 1 teaspoon (4g) pure vanilla extract
    • Fold in the chocolate chips.
      1 cup (180g) semi-sweet 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!

    Notes

    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.
    Click here to add your own private notes.
    Calories: 298kcal | Carbohydrates: 37g | Protein: 6g | Fat: 15g | Saturated Fat: 8g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 4g | Trans Fat: 0.3g | Cholesterol: 50mg | Sodium: 299mg | Potassium: 144mg | Fiber: 3g | Sugar: 20g | Vitamin A: 287IU | Calcium: 80mg | Iron: 2mg
    Did you make this recipe?Mention @wondersofcooking or tag #wondersofcooking!

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    Reader Interactions

    Comments

    1. Shenoa

      April 15, 2025 at 4:38 pm

      5 stars
      Perfect recipe and actually works! The muffins turned out beautiful!

      Reply
      • madison

        April 16, 2025 at 11:34 am

        Yay! I'm so glad to hear you loved the muffins, Shenoa! It's comments like these that keep me going. 🙂

        Reply
    2. Lindsey

      February 01, 2025 at 7:50 pm

      5 stars
      My kids LOVED these! I did mini muffins with a cook time of about 15 minutes. Thank you for sharing!

      Reply
      • madison

        February 08, 2025 at 6:11 pm

        I love that idea! Just like those addictive Little Bites. Thanks so much for sharing your success.

        Reply
    5 from 3 votes (1 rating without comment)

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    Hi, I'm Madison! Welcome to my little cottage kitchen. I'm a self taught gluten-free baker, recipe developer, food photographer, and writer of fact (this blog) and fantasy (creative works in progress). Here you'll learn how to cook from scratch using only wholesome ingredients, making recipes the entire family will love. Every recipe here is a favorite of mine, and I never let gluten-free hold me back.

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