Double Chocolate Sourdough Muffins
These double chocolate sourdough muffins are the best muffins you'll ever make with your sourdough starter discard.
Chock-full of chocolate chips so there's extra chocolate in every bite. They practically melt in your mouth!
The batter can be mixed and baked right away OR fermented overnight in the fridge.
They bake up just like big, bakery-style muffins that are ultra moist!

This AMAZING recipe for double chocolate sourdough muffins is a delicious way to use your unfed sourdough starter discard.
The addition of cocoa powder and chocolate chips makes them irresistible.
A sourdough recipe that's sure to become one of your favorites!
This muffin recipe makes 16 double chocolate sourdough muffins.
Because these muffins freeze great, we like to make a double batch and freeze some for later. They are easy to thaw out for a quick breakfast, snack or dessert.
What you'll need for sourdough chocolate muffins
For this recipe, we modified our sourdough banana nut muffins by removing the bananas and butter and replacing them with extra sour cream and oil to keep the muffins super moist.
We also added cocoa powder and chocolate chips for a rich deep chocolate flavor.
- all-purpose flour
- cocoa powder
- baking soda
- baking powder
- salt
- vegetable oil*
- granulated sugar
- eggs
- sour cream*
- milk*
- vanilla extract
- unfed sourdough starter discard
- chocolate chips
Here are a few ways to modify the recipe if needed:
- We prefer to use avocado oil for our recipes because it has a neutral flavor. Avocado oil can be replaced with either melted butter or melted coconut oil. Do not use solid coconut oil in this recipe as it will not mix into the batter evenly.
- Sour cream can be replaced with full-fat, plain greek yogurt.
- We use unsweetened almond milk to help thin down the batter but feel free to choose from whole milk, skim milk, or any plant-based milk.
- Because this recipe is made with a ยฝ cup sourdough starter that hasn't been fed, it's a great way to make sure that your sourdough discard never goes to waste. But, it can also be used with a sourdough starter that is active. You will still need to use baking soda and baking powder for the muffins to rise.
- If you like nuts, try adding a ยฝ cup of chopped pecans or chopped walnuts for a different flavor variation.
- For the best texture, we do not recommend using whole wheat flour or bread flour.
Helpful equipment
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How to make double chocolate sourdough muffins

The batter is made without the use of a stand mixer. All you need is a few bowls, a whisk, and a spatula to mix the batter. (The recipe makes 16 muffins)
NOTE: The muffins will bake at 425ยฐF (218ยฐC) for the first 5 minutes and at 350ยฐF (176ยฐC) for the remaining 15 minutes. The initial higher temperature will help to give the muffins a bigger oven spring.
Preheat the oven to 425ยฐF (218ยฐC) and place the oven rack in the center position. Line a muffin tin with paper liners.
In a large mixing bowl, whisk together the AP flour, cocoa powder, baking soda, baking powder, and salt. Set the bowl aside.
In a separate bowl mix the wet ingredients. Use a whisk to combine the oil, sugar, eggs, sour cream, milk, vanilla extract, and sourdough starter discard. Mix until the ingredients come together and are smooth.
Pour the wet ingredients into the bowl with the dry ingredients and mix the batter until it just comes together. Do not over-mix the batter.
Add the chocolate chips and stir until they are evenly distributed in the batter.
Use an ice cream scooper to fill the liners. The batter should come to the top of the liner for bigger muffins. Sprinkle a few chocolate chips on top of each one if you want even more chocolate flavor!
Bake the muffins for the first 5 minutes at 425ยฐF (218ยฐC) in the preheated oven. Lower the oven temperature to 350ยฐF (176ยฐC) and continue to bake the muffins for an additional 15-18 minutes.
A toothpick inserted into the center should come out clean when they are done.
Remove the muffins from the oven and allow them to cool completely in the muffin tin or transfer them to a wire rack.

How to store them
If you have leftovers, store them in an airtight container at room temperature for up to 5 days or in the fridge for up to a week.
They freeze great too! Just wrap them individually in plastic wrap and place them into a freezer-safe container to avoid freezer burn. The sourdough muffins will stay fresh for up to 3 months in the freezer.
More sourdough discard recipes
- sourdough morning glory muffins
- sourdough blueberry muffins
- lemon poppy seed sourdough muffins
- sourdough pop tarts
- sourdough chocolate chip cookies
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Double Chocolate Sourdough Muffins
INGREDIENTS
- 2 cups (240 g) all purpose flour
- ยฝ cup (45 g) cocoa powder (regular or dark)
- 2 teaspoons baking powder
- ยฝ teaspoon baking soda
- 1 teaspoon (5 g) salt
- ยฝ cup (125 g) unfed sourdough starter
- ยฝ cup (120 g) avocado oil (or vegetable oil)
- 1 cup (200 g) granulated sugar
- 2 large eggs
- ยพ cup (185 g) sour cream
- 2 teaspoons (10 g) vanilla extract
- ยผ cup (60 g) milk
- 1 ยพ cups (315 g) semi-sweet chocolate chips
INSTRUCTIONS
- Preheat the oven to 425ยฐF (218ยฐC) and place the oven rack in the center position. Line a muffin tin with paper liners.
- In a large mixing bowl, whisk together 2 cups AP flour, ยฝ cup cocoa powder, ยฝ teaspoon baking soda, 2 teaspoons baking powder and 1 teaspoon salt. Set the bowl aside.
- In a separate bowl mix the wet ingredients. Use a whisk to combine the ยฝ cup of oil, 1 cup sugar, 2 eggs, ยพ cup sour cream, ยผ cup milk, 2 teaspoons vanilla extract and ยฝ cup of sourdough starter discard. Mix until the ingredients come together and are smooth.
- Pour the wet ingredients into the bowl with the dry ingredients and mix the batter until it just comes together. Do not over mix the batter. Add the chocolate chips and stir until they are evenly distributed in the batter.
- Use an ice cream scooper to fill the liners. The batter should come to the top of the liner for bigger muffins. Sprinkle a few chocolate chips on top of each one if you want even more chocolate flavor!
- Bake the muffins for the first 5 minutes at 425ยฐF (218ยฐC) in the preheated oven. Lower the oven temperature to 350ยฐF (176ยฐC) and continue to bake the muffins for an additional 15-18 minutes. A toothpick inserted into the center should come out clean when they are done.
- Remove the muffins from the oven and allow them to cool completely in the muffin tin.



Absolutely delicious muffins!! I followed some commenters advice and waited to add baking soda/powder and chocolate chips until after chilling in the fridge overnight. I got worried because the batter was so thick chilled, but I had nothing to worry about they turned out phenomenal. Seriously the best chocolate muffins Iโve ever made (maybe ever eaten) I over filled my liners and just baked 12 muffins, they baked up tall and beautiful. Will absolutely make these again.
I made mini muffins for my gkids. These are just what youโd expect from the perfect chocolate muffin!
These are the best chocolate chip muffins. My grandkids are so picky and absolutely loved them. Definitely will be making again. Thank you for the recipe.
These are delicious!!! Love that they have the added nutrient benefit of being sourdough, gives me an excuse to use all the discard I canโt bear to throw out ๐ I made several batches to freeze for my upcoming postpartum season and my kids and I have already eaten through one so here I am making more at 9 pm and 38 weeks pregnant ๐
Thank you, Mekenzie! We're so thrilled to hear you and your kids love the muffins!
I long fermented these in the refrigerator for about 20 hours and then let the batter warm up slightly before folding in the baking powder, baking soda, and chocolate chips. They baked for the 5 minutes at 425 and then 14 minutes at 350. We were thinking peanut butter chips would be good in them too. Or mint chocolate chips if they're out for the holidays. Thanks for the recipe!
Why did you add these ingredients after the cold ferment?
Delicious but they stuck to the cupcake liners.
Hi Vanessa, we're thrilled you enjoyed this recipe! If your cupcakes are sticking to the cupcake liners, it may be because of the type of cupcake liners you are using. Try spraying them with cooking spray to prevent sticking.
Try spraying the liners with oil!
Perfect recipe. Iโve tried many sourdough muffins but this one beats all of them.
Made this for the first time today and will be an absolute staple recipe that I keep. 10/10 turned out great.
Could I sub the sour cream with Greek yogurt?
Hello!
We haven't tested it with sour cream, so we're not sure exactly how it would come out, but it should be fine! Please let us know ๐
The best muffin out there! I like to do a full fridge ferment so add the leavening agents the next morning before baking. they are delicious every time.
Can you explain how to do this to a new baker ๐