This post may contain affiliate links. Please see our privacy policy for more details.
Jump to RecipeThese double chocolate sourdough zucchini muffins are moist and flavorful. With a hearty serving of vegetables and a double dose of chocolate, these are both nutritious and delicious.

If your family is anything like ours, by this time of year you may feel as though you planted one too many zucchini plants this season and are wondering what to do with your abundance! Now, do not get me wrong we love zucchini.But we have zucchini coming out the ears this year.
I do not know if I lucked out with buying a bag of seeds which are SO good, that the weird weather this season made the zucchini plants thrive, or that I planted them perfectly spaced this year… but we have had zucchini producing nonstop, for over two and a half months!
When we are not enjoying zucchini as a side dish to our meals we have throwing it into our baked goods. From sourdough pancakes to sourdough green waffles and of course, these double chocolate sourdough zucchini muffins, zucchini is making an appearance in nearly everything we cook (and bake).
We love that there is a neutral flavor and a nutritional boost from the extra added vegetables. Just like our green sourdough waffles, this “hidden vegetable“ recipe is one we can not get enough of.
This recipe is inspired by our double chocolate sourdough discard muffins. We swapped out one simple ingredient, the sour cream, with zucchini and man, they are delicious! The addition of the zucchini adds no difference in flavor or texture – but gives us another unique way to enjoy zucchini this season.
And as an added bonus, this is one snack or dessert I love giving to my children because it has some extra vegetables in it (plus the sourdough discard which we all know is great for the gut!).

Why you will love these double chocolate sourdough zucchini muffins
Kitchen Equipment
We used two large bowls, a hand crank grater, a nut milk bag (cheesecloth bag), a muffin pan and a cooling wire rack to make these chocolate zucchini sourdough muffins recipe.

Ingredients for Double Chocolate Zucchini Muffins
The ingredients for these double chocolate zucchini sourdough muffins are pretty straightforward. There are three of the main stars of the show: chocolate, zucchini and sourdough discard.
Make this recipe as a stir and go sourdough recipe or a long fermented muffin recipe.
Chocolate: What would the best sourdough chocolate zucchini muffins be without chocolate? This sourdough chocolate zucchini muffin recipe has both cocoa powder and chocolate chips. We think this makes it double the chocolate, for double the “best” recipe.
Zucchini: We use fresh zucchini from our garden. Keep the skin on and simply grate it before adding it into the recipe. To ensure the liquid ratios are balanced within the recipe we did squeeze the moisture out of the zucchini. This leaves a nice texture, but does not impact the moisture content which is perfectly balanced from the eggs, milk, butter and sourdough discard within the recipe.
Sourdough discard: This recipe uses sourdough discard. If you are wondering which “type” of sourdough discard to use – the recipe can be made with active sourdough or sourdough discard (which can be stored in the fridge). This recipe includes the use of both baking soda and baking powder. The addition of these leavening agents gives the ‘rise’ within these bakery style muffins.
How to make sourdough double chocolate zucchini muffins

Step 1: Stir together dry ingredients.

Step 2: Grate zucchini and squeeze in nut milk bag.

Step 3: Combine wet and dry ingredients.

Step 4: Fill muffin pan and top with both sugar and chocolate chips.

Step 5: Bake and enjoy!
How to store sourdough double chocolate zucchini muffins
Store these muffins on the countertop for up to three days. Alternatively, place them in the fridge in a Ziploc baggie.
You could also place these in the freezer. However, I would recommend placing them in the fridge first with a paper towel. This will help to pull out any additional moisture within the muffins so the bag does not condensate and create ice crystal (resulting in freezer burnt muffins).
To reheat from the freezer allowed to thaw at room temperature or place in the microwave for 10 to 15 seconds to reheat.

Frequently Asked Questions

Double Chocolate Zucchini Sourdough Muffins
Equipment
- 1 Large Bowl
- 1 Rotating Grater
- 1 Silicone Baking Pan
- 1 Nut Milk bag / cheese cloth Can use paper towel or clean dishrag
Ingredients
- 1-3/4 cup All Purpose Flour Spelt flour or gluten free flour can be used as a substitute
- 1 cup White Sugar
- 1/2 cup Cocoa Powder
- 1 tsp Baking Powder
- 1 tsp Baking Soda
- 1/2 tsp Salt If using salted butter, omit!
- 1 cup Chocolate Chips
- 1/2 cup Milk Can substitute with water
- 1/2 cup Zucchini Grated and strained
- 1/2 stick Butter Salted or unsalted. If using melted butter, make sure it is not boiling hot.
- 1 tsp Vanilla Extract
- 1/4 cup Sourdough Discard Active starter or sourdough discard
- 2 Eggs Room temperature
- 2 TBS Turbinado Sugar Optional – For topping muffins
Instructions
Stir and Go Timeline
- Start by preheating the oven to 425 degrees Fahrenheit. Shred the zucchini with a cheese grater or shredder of choice. Place into a nut milk bag, cheesecloth, or paper towels to strain the liquid from the zucchini. Discard the liquid.To the zucchini, combine the remaining wet ingredients.In a separate bowl, combine the dry ingredients except for the chocolate chips.Make a well in the dry ingredients. Add the wet ingredients to the dry and and stir until combined. Fold in the chocolate chips.
- *To make bakery style muffins (AKA tall, muffins), alternate each spot and fill a greased muffin tin. Fill each portion 3/4 of the way full. To make equal muffins – use a large cookie scoop. Sprinkle with turbinado sugar and chocolate chips.
- Bake in the oven for 5 minutes at 425 before reducing the temperature to 350 degrees. Cook for an additional 12-15 minutes, or until the tops are firm to the touch and the centers come out clean when poked with a toothpick.
- Place on a cooling rack to cool completely before storing.
Long Fermented Timeline
- To make long fermented sourdough muffins, combine water and sourdough starter together. This mixture will be a very thick dough and will come together by hand. It will be similar to a 'stiff sourdough starter' in texture. Allow to sit on the countertop for up to 8 hours. The mixture will rise as it ferments.
- After the fermentation is complete, add the remaining ingredients, folding in the chocolate chips last. Ensure there are no clumps in the batter.
- Bake as outlined above in stir and go timeline.
Video
Notes
-
- Ensure the muffin tin is filled at least 3/4 of the way full
-
- Use diary products for rich and decadent muffins
-
- Top the muffins with the flavorings inside the muffins and sprinkle with Turbinado sugar
-
- Bake the muffins in a tin with only 6 at a time.
-
- By giving the muffins more space, they will cook evenly and have more oven spring.
-
- Bake the muffins in a tin with only 6 at a time.
-
- Start with oven temperature at 425 for 5 minutes and reduce to 350 for the remainder of the cooking time to increase oven spring.
Nutrition
Do you like adding zucchini into your baked goods? If you do, what else do you like to use it in? Sourdough zucchini muffins are easily becoming our favorite (with or without the chocolate!). Let us know in the comments below!
