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    Home ยป Recipes ยป Sourdough

    Chocolate Sourdough Muffins

    August 8, 2024 Updated April 29, 2025 BySam 18 Comments

    This post may contain affiliate links. As an Amazon Associate I earn from qualifying purchases. Please read my disclosure policy.
    Jump to Recipe Jump to Video
    collage of sourdough chocolate muffins, top image is a close up of single muffin bite taken out close up, bottom image of multiple muffins tightly placed together

    Sourdough discard makes these chocolate sourdough muffins extra flavorful and tender. Bake them at two oven temperatures for tall, fluffy results! Recipe includes a how-to video!

    Close-up view of chocolate sourdough muffins topped with chocolate chips.

    Sourdough Chocolate Muffins

    We have a growing number of sourdough fans around here lately (yay)! After sharing sourdough pancakes, sourdough brownies, sourdough cookies, and more, lots of you have asked how to incorporate your sourdough discard into even more recipes, like my double chocolate muffins. After some tweaking, we came up with the most irresistible, moist, and chocolatey chocolate sourdough muffins there ever were!

    Why You’ll Love This Recipe

    • Decadent chocolate flavor. We’ll use Dutch process cocoa and bloom it with hot water and instant coffee for good flavor here. And of course, we top the muffins with plenty chocolate chips!
    • Not too dense or heavy. These muffins stay light and fluffy, so they’re not overly indulgent. They are also incredibly moist, thanks to a few key ingredients like sour cream, oil, and brown sugar.
    • Pretty, rounded muffin tops. Nothing is more disappointing than a flat muffin! We’ll use my tried and true technique (borrowed from my chocolate chip muffins and banana muffins) for tall, bakery-style muffin tops.
    • Perfect for using up sourdough discard. This is just one of many sourdough recipes in my growing sourdough recipes collection!

    What You Need

    Before we get started, let’s talk ingredients (and substitutions!).

    Overhead view of labeled ingredients including cocoa powder, sourdough discard, oil, and more.
    • Sourdough discard. If you’re a sourdough fan (I’m not sure why you’d be here otherwise!), you’ll have some of this lying around. If you’re new to the sourdough game but want to get started, head over to my how to make a sourdough starter post!
    • Sour cream. We’ll add this for the same reason we do in my sourdough blueberry muffins; it adds flavor, tenderness, and moisture. If you’d like, you can substitute full-fat, plain Greek yogurt instead.
    • Dutch cocoa. Using Dutch process cocoa provides a smoother flavor and darker color than natural cocoa would. I talk more about this below.
    • Hot water + instant coffee. Both of these will intensify the chocolate flavor of our muffins. You can alternatively use very hot coffee instead, if you don’t keep instant coffee on hand. Whichever you choose, make sure it’s nice and hot because we’ll be using it to bloom our cocoa!
    • Oil. Avocado, canola, or vegetable oil are all good options here. Melted butter could also work instead, but the muffins will be a bit more dense and they won’t stay as moist for as long.

    SAM’S TIP: If you don’t have brown sugar on hand, you might be able to make your own. I have a tutorial on how to make brown sugar that uses just two pantry staples (sugar and molasses)!

    This is just an overview of the ingredients I used and why. For the full recipe please scroll down to the bottom of the post!

    How to Make Chocolate Sourdough Muffins

    Four photos showing sourdough chocolate muffin batter being prepared.
    1. Whisk the dry ingredients and sugar together until combined, then set aside.
    2. Bloom the cocoa: combine the hot water, cocoa, and instant coffee in a large measuring cup.
    3. Add the remaining wet ingredients and whisk until everything is smooth and well incorporated.
    4. Fold the wet and dry ingredients together until 50% combined, then add the chocolate chips. Keep folding until the batter is just combined.
    Two photos showing chocolate muffin batter being portioned into liners and baked.
    1. Divide the batter into a lined muffin tin, filling each mostly full. You will have excess batter if you use a 12-count muffin tin (this recipe makes 17-18 muffins). You can let the extra batter sit on your counter while your first batch of muffins bakes.
    2. Bake until a toothpick comes out clean or with moist/fudgy crumbs and let cool before enjoying.

    SAM’S TIP: Don’t let your muffins cool completely in the muffin tin, or they could end up over-baked or with soggy/greasy muffin liners. I recommend letting them cool in the tin for 5 minutes before (carefully!) removing to a cooling rack.

    Bite missing from a double chocolate muffin made with sourdough discard.

    Frequently Asked Questions

    Can I make these muffins with active sourdough starter?

    Yes! Feel free to substitute an equal amount of active sourdough starter (bubbly, at least 2-3 weeks old if you follow my recipe) for the sourdough discard.

    Do I have to use Dutch process cocoa?

    I personally preferred these chocolate sourdough muffins with Dutch process cocoa, as natural cocoa gave a flatter flavor. Since we are using both baking soda and baking powder, you’d technically be fine to substitute natural cocoa if that’s all you have on hand though.

    Why do you use two oven temperatures?

    Starting at the higher oven temperature encourages our chocolate sourdough muffins to rise nice and tall. We then drop the oven temperature (without opening the door, this is important!) to let the muffins cook through without over-baking.

    If we were to keep the oven at the high temperature the whole time, the muffins would turn out dry. If you were to use the lower temperature, you wouldn’t get the nice rise. Baking is truly a science 😊

    Overhead view of chocolate muffins made with sourdough discard.

    If you don’t have any muffin liners on hand, you can always make your own! I have a tutorial on how to make muffin liners out of parchment paper that’s easy peasy.

    Enjoy!

    Let’s bake together! Subscribe to my newsletter to be notified of all the newest recipes, and find my free recipe tutorials on YouTube 💜

    Close-up view of chocolate sourdough muffins topped with chocolate chips.

    Chocolate Sourdough Muffins

    Sourdough discard makes these chocolate sourdough muffins extra flavorful and tender. Bake them at two oven temperatures for tall, fluffy results!
    Recipe includes a how-to video!
    5 from 7 votes
    Print Pin Rate
    Prevent your screen from going dark
    Course: Breakfast, muffins
    Cuisine: American
    Prep Time: 15 minutes minutes
    Cook Time: 17 minutes minutes
    Total Time: 32 minutes minutes
    Servings: 17 muffins
    Calories: 240kcal
    Author: Sam Merritt

    Ingredients

    • 1 ⅓ cups (165 g) all-purpose flour
    • 1 cup (200 g) light brown sugar
    • 1 teaspoon baking soda
    • ½ teaspoon baking powder
    • ¾ teaspoon table salt
    • ½ cup (118 ml) steaming hot or boiling water
    • ½ cup (50 g) Dutch process cocoa
    • 1 teaspoon instant coffee optional
    • ¾ cup (180 g) sour cream
    • ½ cup (118 ml) avocado oil may substitute canola or vegetable oil
    • 1 teaspoon vanilla extract
    • 1 large egg
    • ½ cup (105 g) sourdough discard
    • 1 cup (170 g) semisweet chocolate chips plus additional for topping, if desired

    Recommended Equipment

    • Muffin tin
    • Mixing bowls
    • Ice cream scoop, for portioning

    Instructions

    • Preheat oven to 425F (220C) and line a muffin tin with paper liners. Set aside.
    • In a large mixing bowl, whisk together flour, sugar, baking soda, baking powder, and salt until well-combined.
      1 ⅓ cups (165 g) all-purpose flour, 1 cup (200 g) light brown sugar, 1 teaspoon baking soda, ½ teaspoon baking powder, ¾ teaspoon table salt
    • In a large measuring cup (or a separate mixing bowl), combine the hot water, cocoa, and instant coffee (if using). Whisk until smooth.
      ½ cup (118 ml) steaming hot or boiling water, ½ cup (50 g) Dutch process cocoa, 1 teaspoon instant coffee
    • Add sour cream, avocado oil, egg, and vanilla extract and whisk well.
      ¾ cup (180 g) sour cream, ½ cup (118 ml) avocado oil, 1 teaspoon vanilla extract, 1 large egg
    • Add sourdough discard to the measuring cup and whisk until ingredients are well incorporated.
      ½ cup (105 g) sourdough discard
    • Add wet ingredients to the flour mixture and use a spatula to gently fold together until about halfway combined. Add chocolate chips and continue to fold until ingredients are just combined.
      1 cup (170 g) semisweet chocolate chips
    • Divide batter into prepared muffin tin, filling each liner nearly to the rim. Note that this recipe makes 18 muffins, if you only have a single 12-count liner it is fine for the batter to sit, covered, on the counter, while the first batch bakes.
    • Sprinkle muffins with additional chocolate chips, if desired, and transfer to center rack of 425F (220C) oven. Bake for 8 minutes, then, without opening the oven door, reduce oven temperature to 350F (175C) and continue to bake for 9-10 minutes longer or until a toothpick inserted in the center comes out clean or with moist/fudgy crumbs (not wet batter).
    • Allow muffins to cool for 5-10 minutes in the muffin tin before gently removing from the tin (careful, the tin is hot! I use a butter knife to gently pry up each muffin) and transferring to a cooling rack to cool completely.

    Notes

    Storing

    Store in an airtight container at room temperature for up to 3 days. Muffins may also be wrapped in plastic wrap and frozen for up to 3 months.

    Nutrition

    Serving: 1muffin | Calories: 240kcal | Carbohydrates: 29g | Protein: 3g | Fat: 13g | Saturated Fat: 4g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 6g | Trans Fat: 0.01g | Cholesterol: 16mg | Sodium: 189mg | Potassium: 145mg | Fiber: 2g | Sugar: 17g | Vitamin A: 82IU | Vitamin C: 0.1mg | Calcium: 43mg | Iron: 2mg

    Nutritional information is based on third-party calculations and should be considered an estimate only. Actual nutritional content will vary based upon brands used, measuring methods, cooking method, portion sizes, and more.

    Tried this recipe? Show me on Instagram!Mention @SugarSpun_Sam or tag #sugarspunrun!

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    Reader Interactions

    Comments

    1. Julie

      May 18, 2025 at 1:46 pm

      5 stars
      These muffins are delicious! It is the best chocolate sourdough recipe I have made. I will be using this recipe exclusively. I have tried many of your recipes and they never disappoint!

      Reply
      • Emily @ Sugar Spun Run

        May 20, 2025 at 4:23 pm

        Thanks so much, Julie! We are so happy you’ve enjoyed everything ๐Ÿฉท

        Reply
    2. Amy

      April 10, 2025 at 4:44 pm

      5 stars
      Alright, people. Just do yourself a favor and don’t even mess around, thinking about not doubling the recipe. I’m here to tell you- that last muffin will disappear before you are ready for it to, and you’ll think to yourself, “Dang, why didn’t I make more of these?” You’re welcome in advance. Now, back to my *double* batch of double chocolate SD muffins.

      Reply
      • Emily @ Sugar Spun Run

        April 11, 2025 at 2:07 pm

        ๐Ÿคฃ We are so happy you love the recipe so much, Amy! Thanks for the review ๐Ÿฉท

        Reply
    3. Laurie E

      March 31, 2025 at 11:18 am

      5 stars
      I was so excited to try this recipe because I just started using my Sourdough starter and I wanted to try and use the discard; additionally, I am always looking for recipes that I can potentially make gluten and sugar free. So I decided that I would make the recipe measuring half regular ingredients and half gluten/sugar free. I was so intent on making sure I got the dry proportions correct that I completely forgot to put in the sourdough starter! But they were both delicious even without it. Just a testament to how talented Sam is with her recipes. Can’t wait to try it again WITH the sourdough starter.

      Reply
      • Emily @ Sugar Spun Run

        March 31, 2025 at 3:49 pm

        Oh no! Hopefully you enjoy them just as much with the starter ๐Ÿ˜Š

        Reply
    4. Kath

      March 23, 2025 at 2:36 pm

      First time I made them and delicious. I used olive oil as did not have other oils. Worked fine. Didnโ€™t even need to sprinkle chocolate chips on top. Thank you

      Reply
      • Sam

        March 25, 2025 at 2:27 pm

        I’m so glad you enjoyed them so much, Kath! ๐Ÿ™‚

        Reply
    5. Ames

      March 15, 2025 at 9:00 pm

      5 stars
      I have made these twice and both times they were stunning. Marvelous. Riding the line between sinful and divine lol.. even excellent if you happen to forget the vanilla ๐Ÿ˜‚

      Reply
      • Sam

        March 17, 2025 at 11:37 am

        I’m so glad you enjoyed them so much, Ames! ๐Ÿ™‚

        Reply
    6. Lynn Tapper

      September 30, 2024 at 5:07 pm

      I cannot eat flour unless it is fermented 72 hours – are your baking recipes able to be fermented that long before baking?

      Reply
      • Sam

        October 01, 2024 at 2:26 pm

        Hi Lynn! It really depends on the recipe. I haven’t tried fermenting these that long, but just thinking about it, I think it could work. Please let me know how it goes if you try it. ๐Ÿ™‚

        Reply
    7. Aubree

      August 09, 2024 at 2:10 pm

      5 stars
      From Hannah (my 6yr old) and Aubree… We love your muffins! My daughter said Sam is always right her recipes are always delicious. That comment is based on you always sampling your work the end of your videos. ๐Ÿ˜†
      We didn’t have Dutch chocolate so we just used cocoa powder and didn’t have instant coffee but it’s still soooooo yummy. Thanks for another sourdough discard recipe. Keep them coming.

      Reply
      • Sam

        August 09, 2024 at 3:58 pm

        Thank you so much, Aubree and Hannah! I’m so glad you’ve both been enjoying everything so much! ๐Ÿ™‚

        Reply
      • Aubree

        March 22, 2025 at 4:42 pm

        5 stars
        It’s been a while since I have made these and I had to come back again to say just how good they are. So delish. They are muffins but almost are like cupcakes with hidden morsels of icing (chocolate chips) instead of on top. These go great with a big glass of cold milk..

        Reply
        • Sam

          March 25, 2025 at 2:31 pm

          I’m so glad you enjoyed them so much, Aubree! ๐Ÿ™‚

    8. Misty

      August 08, 2024 at 6:59 pm

      5 stars
      I slightly overbaked them but they were still great! The sourdough flavor isn’t as deep as your sourdough chocolate chip muffins but it makes sense since dutch chocolate is a rich flavor. Thanks for the recipie! I feel better about eating sugar when sourdough’s involved lol

      Reply
      • Sam

        August 09, 2024 at 4:12 pm

        I’m so glad you still enjoyed them so much, Misty! ๐Ÿ™‚

        Reply
    5 from 7 votes

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    The author (Sam) in blue shirt holding donut Hi, I'm Sam! I'm dedicated to bringing you sweet, simple, and from-scratch dessert recipes. My life may or may not be controlled by my sweet tooth. Send help (or chocolate). Read more about me.

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