Sourdough Chocolate Muffins

5 from 14 votes

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Soft, moist, and extra chocolatey, these decadent sourdough chocolate muffins are everything delicious you could want in a baked goody!

They’re such a fun take on regular chocolate muffins and unbelievably easy to bake — no wait times like other sourdough recipe!

sourdough muffins on wire cooling rack
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Sourdough Chocolate Muffins

I know what you’re thinking… “Sourdough and chocolate? Those don’t mix, do they?!” Trust me, they can and they DO, if done in the right way. Think of your favorite dark chocolate bar and that almost-tart flavor from the bitter pure chocolate. These muffins have a hint of that tartness thanks to using sourdough starter (or discard) in them. If you are maintaining a sourdough starter and don’t want to waste the discard OR have a ton of starter and don’t want to wait to make bread… These yummy chocolate muffins are your answer!

I love to use two 12-cup muffin tins instead of one, and just fill them halfway to create smaller muffins and more of them! It helps for big families (hello!) to make them last longer, and to not waste as much food when little ones can’t finish the big muffins. I hope you love these treats of muffins as much as we do!

sourdough muffin dough in the muffin tin before baking

Sourdough Chocolate Muffin Ingredients:

These sourdough chocolate muffins are a fun baking project with simple ingredients!

Sourdough starter: Or discard — either works to bring the sourdough flavor.

Milk: Milk is the liquid that brings together the batter.

Light oil: You can also use melted butter. This makes the muffins really moist and soft!

Sour cream: Plain Greek yogurt also works; use full fat for super moist muffins!

Egg: An egg helps the batter to rise as it bakes.

Sugar: Sugar adds sweetness to balance the robust sourdough and cocoa flavors.

Vanilla: Vanilla extract brings some warmth to the muffin flavor.

Cocoa powder: This is what makes the muffins brown and chocolatey!

Flour: Flour is needed to create a bread-y, muffin texture.

Baking soda: Soda helps the muffins to puff up as they bake.

Sea salt: Sea salt acts as a balancer among all the sweet and bold flavors.

Chocolate chips: These add bites of extra chocolate throughout and on top of the muffins!

collage of step needed to make muffins

How to Make Sourdough Chocolate Muffins:

Chocolate sourdough muffins are the easiest and I know you’ll love them as much as we do!

  1. Grease a 12-cup muffin tin; preheat the oven to 400 degrees F.
  2. Whisk together the starter or discard, milk, oil, sour cream, and egg.
  3. Add the sugar and vanilla; stir well to combine.
  4. Add the cocoa, flour, baking soda, and sea salt; stir until just combined.
  5. Fold the chocolate chips into the batter.
  6. Divide the batter evenly among the muffin cups.
  7. Sprinkle the tops of the muffins with a few chocolate chips.
  8. Bake the muffins about 20 minutes.
top down view of muffins on a cooling rack

Tips for The Best Sourdough Chocolate Muffins:

Be sure to follow these tips for the best muffins!

  • Don’t over-mix the batter: Mixing the batter too much can lead to dense, tough muffins. Mix until just combined.
  • Fill 2 muffin tins halfway: This creates 24 smaller muffins instead of 12 big ones, which can help them last longer with big families!
  • Check with a toothpick: Because these muffins are dark, it’s hard to tell when they “look” done. After about 20 minutes of baking, insert a toothpick into the center of one muffin. If it comes out clean, they’re finished baking.

How to Store Muffins:

Muffins make great on-the-go breakfasts or snacks! Store them in an airtight container or bag in the fridge for up to 5 days, and enjoy cold, at room temperature, or reheated in the microwave for 30 seconds!

chocolate sourdough muffins with chocolate chips on top

Other Sourdough Recipe You’ll LOVE!

sourdough muffins on wire cooling rack
5 from 14 votes

Sourdough Chocolate Muffins

Soft, moist, and extra chocolatey, these decadent sourdough chocolate muffins are everything delicious you could want in a baked goody!
Prep: 15 minutes
Cook: 20 minutes
Total: 35 minutes
Servings: 12 muffins


  • 1 cup (225g) sourdough starter or discard
  • ¼ cup (85g) milk
  • ¼ cup (56g) light oil or melted butter
  • ¼ cup (60g) sour cream or plain Greek yogurt
  • 1 (50g) large egg
  • 1 cup (200g) granulated sugar
  • 1 teaspoon (4g) vanilla extract
  • cup (28g) cocoa powder
  • 1 1/2 cups (180g) all-purpose flour
  • 1 teaspoon (5g) baking soda
  • 1 teaspoon (6g) fine sea salt
  • 1 cup chocolate chips, (175g), divided
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  • Prepare a 12-cup muffin tin by greasing the cups well. Preheat the oven to 400 degrees F. (205 degrees C.).
  • In a large mixing bowl, add the starter or discard, milk, oil, sour cream, and egg. Use a fork to whisk well to fully combine.
  • Add the sugar and vanilla, and stir well to combine.
  • Add the cocoa, flour, baking soda, and sea salt. Stir until just combined.
  • Add almost all of the chocolate chips to the batter, reserving a few to sprinkle on top of the muffins before baking if desired. 
  • Fold the chocolate chips into the batter.
  • Divide the batter evenly among the muffin cups. If using, sprinkle the tops of the muffins with reserved chocolate chips.
  • Bake the muffins until the tops are firm and the middles cooked through, about 20 minutes.
  • Cool the muffins for 5 minutes in the muffin tin before removing them to cool on a wire rack. Eat warm or at room temperature.


  • I’ll often grease a second muffin tin and bake 24 smaller muffins for about 15 minutes instead of 12 large muffins. This makes them go farther in a bigger family and helps to reduce toddler waste when they can’t finish a bigger muffin. Plus, the smaller muffins fit nicely in lunch boxes. 
  • You can use sour cream or plain Greek yogurt for this recipe. I prefer to use the full fat versions. Reduced fat sour cream or plain Greek yogurt leads to a muffin that is drier in texture.


Serving: 1 of 12 muffins, Calories: 280kcal, Carbohydrates: 44g, Protein: 3g, Fat: 11g, Saturated Fat: 4g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 0.002g, Cholesterol: 19mg, Sodium: 296mg, Potassium: 116mg, Fiber: 1g, Sugar: 26g, Vitamin A: 61IU, Vitamin C: 0.04mg, Calcium: 30mg, Iron: 1mg
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I adore this sourdough chocolate muffin recipe because it’s subtly tart and chocolatey-rich with the perfect amount of chocolate chips to bring the fun!

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Recipe Rating


  1. Tamara Sherriff says:

    5 stars
    Great muffins!! I have been making these muffins for a year. I make them about every fortnight. My partner and two boys love them. Sometimes I don’t put in the cocoa powder to be regular choc chip muffins. My oven cooks them best at 18 minutes. They freeze well!
    Thank you Melissa

  2. Nicolette says:

    5 stars
    Thanks for sharing this recipe. It was a great way to sneak my sourdoughdiscard in on my kids who think it is gross. 😉

  3. Claire H says:

    5 stars
    Very lovely!!! Just made them and shared them with the neighbors…awesome all around! My sourdough discard was a mixture of three I have…An AP flour, a sprouted whole wheat and a rye. Used Casa Papantla vanilla paste, sweet cream butter, Callebaut 100% cocoa powder and Guittard semi sweet chocolate chips. Also added a splash of espresso powder. Will put this in my once a month rotation for sure! Thank you, one of the very best recipes I have tried ever!

    1. Melissa says:

      Ohhhh all of that sounds soooo good! I’ll be your neighbor!

  4. Aubri says:

    I made these for an after school snack today. I made up the batter, and then let them sit out and ferment for about 3-4 hours before baking. Delicious! My kids loved them too. Thank you!

  5. Ces says:

    5 stars
    happy with the recipe, outer texture was interesting over all delicious! Did not even last long on the counter, in an hour 11 muffins were gone! I used 1 large size muffin tin and 2 regular sized ones and I had 3 extra scoops for 3 regular sized muffins. Made 21 muffins with this recipe. Going to make it again and with more chocolate! Thank you for this recipe!

  6. Aubri says:

    5 stars
    Have you tried these doing a longer ferment? I’m just curious how they might turn out. I try to give sourdough some time to work. I’m excited to try this recipe! Thanks!

  7. Marissa Hunt says:

    Have you tried freezing these ?

    1. Melissa says:

      Yep, they freeze great! They get just a bit dry like most other baked goods but it wouldn’t stop me from doing it.

  8. Ruth says:

    5 stars
    Yummy (and easy) recipe!! Chocolate and sourdough are staples at our house… so naturally, i doubled the amount of both and baked in over-sized muffin tins 😁😋 —thanks for sharing!

  9. deb c says:

    5 stars
    I’ve been craving chocolate so I made a batch today. 24 minis and 9 regular size….I love minis…they are so easy to grab one and go and return and go and return and go! I really like the slight twang of the sourdough mixing with the chocolate. Next time…I think I’ll add some chopped pecans in. Thanks!

  10. Kaysha says:

    5 stars
    These are super good and easy to make! I love all the chocolate!