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These chocolate sourdough muffins are rich, fudgy, and loaded with chocolate. Plus they rescue your discard from the compost bin.

You get deep cocoa flavor, a tender crumb, and bakery-style muffin tops, no mixer required. It’s a smart way to use sourdough discard and get homemade muffins that taste like they came from a bakery case.

Two chocolate muffins on top of each other; jar of sourdough starter in background.
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Want more sourdough discard recipes? Our blueberry sourdough muffins and sourdough cake donuts are both easy ways to keep that sourdough starter working.

Here’s Why This Sourdough Chocolate Muffin Recipe Works

One-bowl batter: Minimal cleanup. Just whisk, fold, and bake.

Sourdough discard: Adds depth and moisture without shouting “sourdough.”

Loaded with chocolate: Cocoa and milk chocolate chips. No skimping here.

Bakery-worthy texture: Moist muffins with domed tops, all from a home oven.

A discard chocolate muffin on a plate next to chocolate chips and milk.

Recipe Tips

Use discard at room temp: Cold discard can stiffen the batter. Let it warm up for easier mixing.

Don’t skip the spray: Lightly spraying muffin liners keeps them from sticking to the paper.

Full cups = tall tops: Fill the muffin cups nearly to the brim for that dramatic bakery dome.

Check early: Start checking at 20 minutes. Overbaking dries them out fast.

Weigh your ingredients: Especially the cocoa, discard, and flour. It keeps the texture consistent and prevents dry muffins.

Rest the batter (optional): Letting it sit for 20–30 minutes before baking can give a better crumb and taller domes.

Espresso powder boost: Even if you’re not using the optional espresso powder, consider adding just ¼ teaspoon. It deepens the chocolate flavor without tasting like coffee. Our sourdough chocolate cake uses hot coffee for a similar effect.

A chocolate sourdough muffin on a plate with muffins in the back.

Sourdough Wins Again

These chocolate sourdough muffins hit that perfect balance: easy to make, loaded with chocolate, and a clever way to use up sourdough discard.

If you’re into sourdough baking or just want an easy muffin recipe with big flavor, this one delivers. Try my banana sourdough muffins for something fruity but just as simple.

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Two sourdough chocolate muffins stacked on top of each other.
Prep Time: 10 minutes
Cook Time: 22 minutes
Total Time: 32 minutes
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Chocolate Sourdough Muffins

Rich, moist chocolate sourdough muffins made in one bowl with cocoa, sourdough discard, and chocolate chips. Easy to make, freezer-friendly, and full of flavor.

If you make this recipe, please leave a star rating and comment.

Servings: 12 servings
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Ingredients 

  • cups brown sugar, packed; 266 grams
  • ¾ cup sourdough discard, 170g, 100% hydration
  • 2 large eggs
  • ½ cup milk, 113 grams
  • cup vegetable oil, 66 grams
  • 2 teaspoons vanilla extract
  • cups all-purpose flour, 210 grams
  • cup unsweetened cocoa powder, Dutch processed; 57 grams
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ¾ teaspoon instant espresso powder, optional
  • ¾ teaspoon salt
  • cups milk chocolate chips, 220 grams, or chopped chocolate
  • coarse sugar, for topping (optional)

Instructions 

  • Preheat your oven to 350°F. Line a standard 12-cup muffin pan with paper liners and lightly spray the liners with nonstick spray.
  • In a large bowl, whisk together the sugar, sourdough discard, eggs, milk, oil, and vanilla.
    Mixing the wet ingredients for a sourdough chocolate muffin.
  • Place a sifter over the bowl and add the flour, cocoa powder, baking powder, baking soda, espresso powder (if using), and salt.
    Adding the dry ingredients to the bowl.
  • Gently fold everything together until well combined. Fold in the chocolate chips. Don’t overmix, just make sure there are no dry pockets of flour.
    Mixing the chocolate muffin batter in a bowl.
  • Divide the batter between the muffin cups. They’ll be pretty full, which helps give you that domed top. Sprinkle with coarse sugar if you’d like.
    Adding the sourdough chocolate batter to muffin tins.
  • Bake for 20–25 minutes, or until a toothpick inserted in the center comes out clean.
  • Let the muffins cool in the pan for about 5 minutes, then transfer them to a rack to cool another 10–15 minutes.

Notes

Espresso powder: You can skip it, but even a small pinch boosts the chocolate flavor.
Use Dutch-process cocoa: It gives the richest color and taste.
Weigh your ingredients: Especially flour, discard, and cocoa, to keep the texture light and moist.
Optional rest time: Let the batter sit 20–30 minutes before baking for taller muffins.
Longer fermentation: You can refrigerate the batter for 3 to 4 hours before baking. It holds up well and still gives great rise.
Freezer-friendly: Cool completely, then store in a zip-top bag for up to 2 months. Thaw at room temp or warm briefly in the microwave.
Molten muffin option: This recipe was adapted from our molten chocolate muffins, and you can use the fudge filling technique from that recipe if you want a gooey center.

Nutrition

Serving: 1 serving, Calories: 363kcal, Carbohydrates: 57g, Protein: 5g, Fat: 14g, Saturated Fat: 6g, Polyunsaturated Fat: 4g, Monounsaturated Fat: 2g, Trans Fat: 0.04g, Cholesterol: 29mg, Sodium: 294mg, Potassium: 216mg, Fiber: 2g, Sugar: 36g, Vitamin A: 56IU, Calcium: 80mg, Iron: 2mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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Ingredients used to make chocolate sourdough muffins.
Several muffins on a cooling rack.

About Dahn Boquist

Dahn Boquist is a retired nurse turned recipe developer, home cook, and baker with years of hands-on experience creating and testing from-scratch recipes. She specializes in whole-food cooking with creative twists on classic dishes. When she’s not in the kitchen, she enjoys sharing meals with family, exploring the Pacific Northwest, and spending time with her grandchildren.

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