These Chocolate Sourdough Zucchini Muffins are packed with summer zucchini but taste like a delicious, moist chocolate muffin! The sourdough discard also gives these muffins a bit of tang, which is a nice complement to the chocolate.
These muffins are perfect for breakfast or brunch, or even a sweet afternoon treat (and kids love them, too!).
And if you have a ton of zucchini on hand, try this Sourdough Zucchini Bread and these Zucchini and Sweetcorn Fritters.

Why you'll love this recipe
- Both kids and adults will love these Chocolate Sourdough Zucchini Muffins! And they're packed with zucchini, but you wouldn't know it!
- Looking for other veggie-packed recipes? Try these Sourdough Sweet Potato Waffles and these Sourdough Pumpkin Muffins.
- This recipe uses sourdough discard, but you could easily modify to use active sourdough starter instead, if you prefer.
- These muffins use cocoa powder and chocolate chips for that extra chocolate flavor.
- Muffins freeze well, so you can enjoy some now and freeze the rest for later!
Jump to:
Ingredients
There are only a few key ingredients you'll need to bring this recipe together.

- Cocoa powder: Use unsweetened cocoa powder for this recipe.
- Chocolate chips: I suggest milk chocolate or dark chocolate chips. Chocolate chunks work, too!
- Zucchini: It's important to press out as much moisture from the zucchini as possible to get the right texture and moisture content in the batter. You can do this between layers of paper towels, or gather the shredded zucchini into a ball, wrap it in paper towels or a clean kitchen towel, and wring out the moisture.
- To shred the zucchini, use the large holes of a box grater, or the shredding attachment on a food processor or other appliance.
- A lot of zucchini to use? You might also love this Sourdough Zucchini Cake and these Sourdough Zucchini Waffles!
- Sourdough discard: The sourdough discard should be unfed and at room temperature for this recipe. This recipe is designed for a sourdough starter that uses a 1:1 ratio (when you feed your starter, it's with 1 part flour and 1 part water). If your starter uses a different ratio, you may need to adjust some of the ingredients in this recipe.
- Learn more about how to make a homemade sourdough starter.
See full recipe below for detailed directions.
Substitutions & Variations
This is a very adaptable recipe and below are a few easy substitutions and variations you can try.
- Use active sourdough starter - If you want to make this recipe with active sourdough starter, you can. To do so, replace the sourdough discard with active starter (200g). You will not need to change any other ingredients in the recipe.
- Use other summer squash - Zucchini is great for this recipe, but you could also make it with yellow squash for a slightly different flavor profile.
- Add nuts - Add ½ chopped walnuts when you're folding in the zucchini and chocolate chips.
- Try a chocolate zucchini cake - Interested in this recipe in a cake version? Try this Sourdough Chocolate Zucchini Cake.
I have not tested this recipe with other variations, but if you do, let us know how it turns out in the comments! I always love to hear how you're adapting these recipes and use those as ideas for future recipes as well!
How to Make Chocolate Sourdough Zucchini Muffins
There are a few simple steps to bring this recipe together! The full recipe with detailed directions is at the bottom of this post.

- Step 1: Shred and drain your zucchini. Set aside.

- Step 2: Cream together the butter and sugar.

- Step 3: In a separate bowl, mix together the remaining dry ingredients. Then, mix together the wet ingredients. Combine the wet and dry ingredients in the bowl with the butter mixture.

- Step 4: Fold in the zucchini and chocolate chips.

- Step 5: Using a cookie scoop, fill lined muffin cups with batter (about ⅔ full). Sprinkle with turbinado sugar.

- Step 6: Bake for 30-35 minutes, or until a toothpick inserted in the center comes out clean. Let cool slightly, then serve.
Expert Baking Tips
- Remove excess moisture from the zucchini. Press the shredded zucchini between layers of paper towels, or gather the zucchini into a ball, wrap in paper towels, and wring out the excess water.
- Don't overmix the batter. Stir ingredients just until combined, you don't need to do any extra mixing!
- Use muffin liners. I find using muffin liners gives a better shape to the muffin. I like these tulip muffin liners the best!
- Use a cookie scoop to fill the muffin cups. It's so much easier than battling a spoon!
- Looking for other summer baking recipes? Try this Sourdough Discard Strawberry Cake and this Sourdough Peach Cobbler!
Storage
Room Temperature Storage: Store muffins in an airtight container at room temperature for up to 3 days. You can reheat them in the microwave for 15-30 seconds to make them warm and soft again.
Freezer Storage: Let them cool completely, then transfer to an airtight container or bag and freeze for up to 3 months. To reheat, let the muffins thaw at room temperature, or reheat in the microwave for 30-60 seconds until they're warm and soft again.

Recipe FAQs
Yes, you can. To do so, replace the sourdough discard with active sourdough starter. You don't need to make any other modifications to the recipe.
I suggest shredding zucchini on the large holes of a box grater. Alternatively, you could also use the shredding attachment on a food processor or another kitchen appliance with shredding capabilities.
I like to press the shredded zucchini between layers of paper towels. It also works well to gather the shredded zucchini into a ball, wrap it in paper towels or a clean kitchen towel, then wring out as much liquid as possible.
More Sourdough Discard Breakfast Recipes
If you tried these Chocolate Sourdough Zucchini Muffins or any other recipe on my website, please leave a ⭐ star rating and let me know how it went in the comments below. I'd love to hear from you! Happy Baking!

Chocolate Sourdough Zucchini Muffins
Ingredients
- ¼ cup unsalted butter softened
- 1 cup granulated sugar
- 1 cup + 2 Tablespoons all-purpose flour
- ½ cup unsweetened cocoa powder
- 1 ½ teaspoons baking powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- 200 grams (about ¾ cup) sourdough discard unfed, at room temperature
- 2 eggs
- ¼ cup vegetable oil
- 2 teaspoons vanilla extract
- 1 ½ cups zucchini shredded and drained
- 1 cup chocolate chips
- 1-2 Tablespoons Turbinado sugar for topping, optional
Instructions
- Preheat oven to 375℉ (190℃) and line a 12-cup muffin pan with muffin liners.
- Shred your zucchini on the large holes of a box grater. Press the shredded zucchini between layers of paper towels to remove excess moisture. Set the zucchini aside.
- In a large mixing bowl, cream together the softened butter and granulated sugar until light and fluffy, about 2 minutes.
- In a small bowl, whisk together the flour, cocoa powder, baking powder, baking soda, and salt.
- In a third bowl, whisk together the sourdough discard, eggs, vegetable oil, and vanilla extract.
- Add the dry ingredients and liquid ingredients to the creamed butter mixture. Stir until almost all the dry spots are gone (do not overmix!).Fold in the shredded zucchini and chocolate chips, mixing until combined.
- Use a spoon or cookie scoop to fill the lined muffin cups about ⅔ full with batter. You'll likely have enough batter for an extra 1-2 muffins (about 14 muffins in total). Sprinkle with turbinado sugar (optional).
- Bake for 30-35 minutes until a toothpick inserted in the center comes out clean. Let cool for 5 minutes in the pan, then serve or transfer to a cooling rack to cool fully.
Enid Santos says
Oh my goodness. I made the most delicious chocolate sourdough zucchini muffin, I will definitely be making this again. Love them so much! They key to a delicious muffin is GREAT and QUALITY INGREDIENTS.
Jessica Vogl says
Love the chocolate and zucchini combination. A hit with both adults and kids at our house!