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.
Meredith says
This recipe is fantastic. I even use some of the batter to make a small loaf to see how it would bake and it came out fantastic. I used olive oil and low fat sour cream, 1% milk and my whole family loved them!
Cecilia Ortiz says
I replaced the oil with softened butter and they were delicious.
Brittanie says
This was my very first sourdough discard recipe and while it wasn’t perfect it was simple and fun! The muffins are definitely delicious 🥰
Ashten says
Some of the most delicious muffins I’ve ever made and had that delicious “muffin top” action! Will definitely make these again. Thank you for sharing!
Stacie says
I can’t wait to try these for my daughters birthday! I’m wondering if you use your homemade cashew sour cream in this recipe? Or if that would turn out good?
Amy says
Hi Stacie, I haven't tried it but I think it could do the trick!
Amber says
Anybody that knows me, knows that I am obsessed with double chocolate muffins.
I knew I had to try this recipe when I came across it. These are hands down the best muffins that I have ever had. I've made them 4 times now. My 10-year-old says that they are "s-tier and I can never stop making them." haha
I dont even want to give it a review because it is so good. I almost want to keep it a secret. It deserves every star that you could possibly give it.
Lucia smith says
The recipe for double chocolate sourdough muffins is a nice read. However, I wish to try it with ghee baking as ghee offers a higher smoke point than vegetable oil and boiling points of oils are lower than ghee butter. I prefer using Milkio grass-fed ghee for all culinary purposes.
Christine Dix says
We don't use vegetable oils, what can I sub there?
Also, is there a sub for sour cream? Yogurt?
Amy says
You could use melted coconut oil or avocado oil (I use avocado oil). You can use greek yogurt in place of sour cream.
Eve says
If I want to let it ferment overnight, should I keep the baking soda and powder out and mix them in right before I'm ready to bake the muffins? Thank you for the recipe!
Amy says
You can mix them into the batter and let ferment in the fridge.
Eve says
Thank you so much! Can't wait to try it out! 🙂
Mariela says
the best chocolate muffins ever!