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! If you love these you’ll also love these Apple Cinnamon Muffins!

sourdough muffins on wire cooling rack
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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!

Table of Contents:


sourdough muffin dough in the muffin tin before baking

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!

See recipe card below for full information on ingredients and quantities

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.
top down view of muffins on a cooling rack

Frequently Asked Questions:

How to store sourdough muffins?

Sourdough 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.

Can I reheat sourdough muffins?

Yes! You may enjoy them cold, at room temperature, or reheated in the microwave for 30 seconds!

chocolate sourdough muffins with chocolate chips on top

More Sourdough Recipes to Consider:

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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5 from 14 votes

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Recipe Rating


  1. Fredric says:

    5 stars
    I bake at 350. If baked at 400 sometimes there is dough still in the middle. It takes a bit longer so check it.

  2. Angie says:

    Out. Of. This. World!! Thank you so much for such a delicious recipe!!
    I did alter a couple of things but nothing major.
    Instead of 1/4 cup of milk, I substituted for 1/2 cup almond milk.
    Instead of 1/4 cup of oil, I used 1/4 cup of applesauce.
    I baked mine for 25 minutes

    Perfection!! Saving this recipe! TODDLER APPROVED!
    Thank you!

    1. Melissa says:

      Yay! Thank you for letting us know what worked for you, it’s so helpful!

  3. Keri says:

    These were very good. I had to add more milk due to my starter being very thick. Used half the amount of chocolate chips and only 3/4 cups sugar. Over baked a bit because my muffin cups are on the smaller side. Still tasted very yummy! Thanks for sharing!

  4. Manon says:

    5 stars
    Amazing recipe! I autolyse the flour with the starter, the yogurt and the milk for at least 8 hours before putting the rest of the ingredients to get the benefit of the sourdough. The taste is out of this word, and no need for chocolate chips. Thanks!

  5. Evangelia says:

    5 stars
    ‘ Amazing recipe. Always a hit with the family. Love that it is not too sweet. Perfect for breakfast. I bake smaller bite size muffins in a silicone tray. Works fine.

  6. Annita says:

    5 stars
    I use silicone baking cups; no mess, no papers, no greasing. Safflower oil (healthy alternative and no change in moisture of muffin). NF Greek yogurt–made no significant difference this last time rather than the whole fat sour cream. Decrease sugar 1/4 cup…stronger chocolate flavor without bitterness. Sometimes a pinch of instant espresso granules (deepens chocolate flavor). Sometimes a pinch of cinnamon (just a small pinch–almost unnoticeable, but there is a subtle flavor adding a kick). These are my favorite go-to wonderful-almost birthday cake quality dessert… Hot out of oven, split in half, topped with fresh strawberries and ice cream…drizzle just a hint of chocolate sauce–amazing sundae! Also easy to make a half batch.. OH__and YES! they freeze well, and thaw in microwave 30 seconds coming out as if fresh baked.

    1. Melissa says:

      Thank you for sharing what worked for you! That’s so fun and it sounds amazing with strawberries!

  7. Erin says:

    5 stars
    These are delicious and moist! I love that it uses 1c of sourdough discard!

  8. Carrie Martin says:

    5 stars
    How would I bake these if I used a 6 jumbo muffin pan?

    1. Melissa says:

      Probably double, what you are looking for is the muffin to spring back when you lightly touch it. If you touch it and it stays indented, it’s not baked all the way yet.