With a rich chocolate taste, these double chocolate sourdough muffins have an easy batter, are packed with chocolate chips, and stay fresh and moist for days after you bake them.

Use your regular sourdough starter or try it with chocolate sourdough discard.
Recipe includes both cup and metric measurements. Choose your preferred method on the recipe card.
Ingredients and substitutions

Espresso: Use espresso or strong brewed coffee (it can be decaf!). Adding coffee when making a recipe with cocoa powder enhances its flavor (I also do this in my famous sourdough chocolate cake).
If you don’t want to use coffee, replace it with more milk.
Sourdough discard: Use regular sourdough discard or leftover chocolate discard if you have some. Both create delicious, moist muffins—though the chocolate starter makes them even richer!
You can also use an active sourdough starter if that’s what you have.
Oil: Use vegetable, avocado, or your preferred oil, but avoid strong-tasting oils like olive oil. You can swap it for butter, but that will make drier muffins.
Baking soda: Check that your baking soda hasn’t expired. Using baking soda instead of baking powder creates a darker muffin.
Chocolate chips: I prefer semi-sweet or dark chocolate chips, but you can swap them for milk chocolate chips, peanut butter chips, or even white chocolate chips.
Cocoa powder: Use 100% cocoa powder for the best chocolate flavor.
How to make them
You can use ingredients straight from the fridge: no need to let them warm up to room temperature!
Step 1. Add cocoa powder to a large bowl. If it’s lumpy, sift it first. Pour hot milk over the cocoa powder and whisk until smooth.
Step 2. Whisk the remaining wet ingredients into the batter: espresso, Greek yogurt, oil, brown sugar, vanilla extract, egg, and sourdough discard. Stir until fully combined.
Step 3. In a medium bowl, mix the flour, salt, and baking soda. Add this to the batter and whisk until no dry flour remains.
Step 4. Stir in ¾ of the chocolate chips, saving the rest to sprinkle on top.
Step 5. Use a large spoon or an ice cream/cookie scoop to fill the muffin cups about ¾ full with batter. Sprinkle the remaining chocolate chips on top.
This recipe makes 12 muffins, and can easily be doubled.
Step 6. Preheat the oven to 425°F (220°C). Position the rack in the middle, then bake the muffins for 5 minutes. Reduce the temperature to 375°F (190°C) and continue baking for about 15 minutes, or until a toothpick inserted in the center comes out with crumbs but no wet batter.
When the muffins finish baking, take them out of the oven and let them cool in the pan for 5 minutes. Then, transfer them to a cooling rack and let them cool for another 10 minutes before serving.
Store the muffins properly, and they’ll stay fresh for about 4 days (just like most of my sourdough baked goods). Once they’ve cooled completely, place them in an airtight container and keep them away from sunlight.
Tips for the best muffins
- Bake at a high temperature for the first 5 minutes! This helps the batter rise better than baking at a steady lower temperature.
- If this is your first time making these muffins, check for doneness after a total of 15 minutes. Don’t mistake melted chocolate for raw batter!
- Keep the oven door closed during the first 10 minutes of baking.
- Avoid overfilling the muffin cups to prevent batter overflow.
- Use all-purpose flour for this recipe. Bread flour or whole wheat flour won’t produce muffins as soft as all-purpose flour does.
- For a flavor twist, swap half of the chocolate chips for chopped hazelnuts or almonds (both pair great with any chocolate recipe).
Have you tried these Sourdough Chocolate Muffins? Please leave a 🌟 star rating in the recipe card below, I'd love to know how it went!
📖 Recipe
Chocolate Sourdough Muffins
Equipment
- 1 muffin tin
- 12 muffin paper cups
Ingredients
- 60 g cocoa powder 100%
- 185 g milk hot
- 30 ml espresso or strong brewed coffee
- 120 ml vegetal oil or avocado oil
- 200 g brown sugar
- 1 large egg
- 1 teaspoon vanilla extract
- 135 g Greek yogurt
- 120 g sourdough starter discard or chocolate sourdough starter/discard
- 200 g all-purpose flour
- 1 ¼ teaspoon baking soda
- ¼ teaspoon fine sea salt
- 300 g chocolate chips
Instructions
- Preheat the oven at 425°F (220°C), rack positioned in the middle.
- In a large bowl, add cocoa powder. You can sift it if it’s too lumpy. Bloom the cocoa powder by adding hot milk over it, whisking until the ingredients are fully combined.
- Whisk the remaining wet ingredients into the batter: espresso, Greek yogurt, oil, brown sugar, vanilla extract, egg, and sourdough discard, whisking them together until combined.
- In a medium bowl, mix flour, salt, and baking soda. Add this to the batter, whisking until all the flour is absorbed and no dry lumps remain.
- Add ¾ of the chocolate chips, saving some for topping the muffins.
- With the help of a large spoon or ice cream scoop/cookie dough scoop, fill the muffin cups until they are about ¾ full with the batter, then top them with the remaining chocolate chips.
- Bake for 5 minutes at 425°F (220°C), then lower the temperature to 375°F (190°C) and bake for about 15 minutes more, or until you insert a toothpick in the middle and it comes out with crumbs only, not runny batter.
- When baked, remove the muffins from the oven and wait for about 5 minutes before transferring them to a cooling rack. Wait another 10 minutes before serving.
Video
Notes
- If you don’t want to use coffee, replace it with more milk.
- You can use an active sourdough starter if that’s what you have.
- Use vegetable, avocado, or your preferred oil, but avoid strong-tasting oils like olive oil. You can swap it for butter, but that will make the muffins less moist.
- I prefer to use semi-sweet or dark chocolate chips, but you can swap them for milk chocolate chips, peanut butter chips, or even white chocolate chips.
- You can substitute Greek yogurt with sour cream. Both can be fat-free.
- If this is your first time making these muffins, check for doneness after a total of 15 minutes and don’t mistake melted chocolate for raw batter.
- Keep the oven door closed during the first 10 minutes of baking.
- Avoid overfilling the muffin cups to prevent overflow.
- Use all-purpose flour for this recipe. Bread flour or whole wheat flour won’t produce muffins as soft as all-purpose flour does.
Audrey
These were SO GOOD!! No leftovers!
Susan
Can these be mad Gluten free?
Tatiana Kamakura
Hi Susan,
I’ve made a similar recipe before using Bob’s Red Mill 1:1 gluten-free flour, and it turned out good! You might want to give it a try if looking for a gluten-free wheat flour option. Hope that helps!