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 ½ 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 ½ 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 425°F (218°C) for the first 5 minutes and at 350°F (176°C) for the remaining 15 minutes. The initial higher temperature will help to give the muffins a bigger oven spring.
Preheat the oven to 425°F (218°C) 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 425°F (218°C) in the preheated oven. Lower the oven temperature to 350°F (176°C) 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
- ½ cup (45 g) cocoa powder (regular or dark)
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- 1 teaspoon (5 g) salt
- ½ cup (125 g) unfed sourdough starter
- ½ cup (120 g) avocado oil (or vegetable oil)
- 1 cup (200 g) granulated sugar
- 2 large eggs
- ¾ cup (185 g) sour cream
- 2 teaspoons (10 g) vanilla extract
- ¼ cup (60 g) milk
- 1 ¾ cups (315 g) semi-sweet chocolate chips
INSTRUCTIONS
- Preheat the oven to 425°F (218°C) 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, ½ cup cocoa powder, ½ 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 ½ cup of oil, 1 cup sugar, 2 eggs, ¾ cup sour cream, ¼ cup milk, 2 teaspoons vanilla extract and ½ 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 425°F (218°C) in the preheated oven. Lower the oven temperature to 350°F (176°C) 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.
G says
I made this with monk fruit and erythritol sweetener, sugar cree chips; so hood!! Thanks again for another wxcellent recipe!
T says
Could the sour cream be swapped for plain Greek yogurt?
Amy says
Yes it can.
kayla perry says
I almost always tweak peoples recipes to my liking… but I took one look at this recipe and knew it needed no adjustments. I was right! These muffins came out perfectly delicious! (I did substitute melted butter for avo oil, simply because i didn’t have any high temp oils on hand)** For fun, i sprinkled a bit of espresso grounds on a couple, and they were yummy but they are truly perfect as is. Little Spoon Farm recipes are so delicious and this one is no exception!
Alyssa says
Made a double batch of these and substituted Carmel bits for the second measure of chocolate chips and now my kids are volunteering me for bake sales. Definitely recommend!
Christine Arendas says
This recipe is the best chocolate muffin recipe ever. So moist and light even though I used organic sprouted spelt flour only. Also cut the sugar down to 3/4 cup coconut sugar, yoghurt for the sour cream and I only used 1 cup carob chips and carob powder for the cocoa. Next time I will replace the oil for apple sauce to make it more healthy.
Amy says
Thanks for sharing Christine! 🙂
Julie says
Easy to make and delicious! A great way to use sourdough discard. Tastes like a really good chocolate cake. I think I might bake it in a bundt pan next time.
Robin says
I'm new to sourdough baking and this was the first thing that I made. They were absolutely fantastic! Moist and delicious!
Debe says
I didn’t see any notes about fermenting overnight. I need to do that as my grandkids are gluten intolerant and need the extra fermentation breakdown. Do you just mix the batter together and allow it to ferment overnight?
Amy says
Mix the batter and let it ferment for a few hours and then pop it in the fridge for a cold ferment until you're ready to bake.