Sourdough Discard Chocolate Chip Muffins

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These delicious and healthy sourdough chocolate chip muffins are long fermented, perfectly sweetened, and they offer a pleasant, fluffy texture. Mix them up the night before and bake the next day. Great way to use extra sourdough discard.

sourdough chocolate chip muffin on a white place with chocolate chips sprinkled on the plate. More muffins in the background on a wood cutting board

We are still rolling with the sourdough recipes over here, y’all. Did you see the sourdough chocolate chip cookies or scones yet? Yum!

This one was slightly trickier to get down. It’s hard to long ferment a recipe with eggs. 

You could just whip this up without the fermentation process, but then you wouldn’t be reaping the health benefits of the fermentation.

Nor would my family be able to tolerate the muffins.

I used to think long fermentation was a nuisance, but I’ve come to find it super convenient, actually. 

Just mix together some of the ingredients, then allow the dough to sit for a while (12 to 24 hours) before baking. 

No need for an hour-long commitment of mixing and baking all in one sitting. (Although with these muffins you totally can mix them together and bake right away, because I tried it).

I’m telling you, once you get the hang of it, sourdough is the way to go.

Delicious and healthy. Not only do these muffins have fermented grains, but they are sweetened with honey, as well.

These will probably be on weekly rotation. These chocolate chip sourdough muffins make the perfect snack, breakfast, or dessert.

Recipe Highlights:

Fluffy, moist, and delicious muffins: They are super yummy and made with simple ingredients.

Super easy to make. Mix the night before and bake the next day for a quick breakfast. Also makes a great snack.

Great way to use leftover sourdough discard. Did you know you can totally use sourdough starter discard to ferment grains, it doesn’t have to be an active starter (although you can use active as well).

Long fermented for better digestion (if desired).

Master muffin recipe: Don’t want to use chocolate  chips? No biggie, swap them out for different muffin add-ins like blueberries, cranberries, raspberries, white chocolate chips, etc.

overhead shot of sourdough chocolate chip muffins on a wood cutting board.

Tips For Making This Recipe:

  • There are definitely tricks to these muffins. Since the dry ingredients (grains) are soaked, they tend to firm up after the soaking. The eggs are added after and need to be incorporated well.
  • I like to use the stand mixer to mix up this recipe. You can also use your hands to start breaking up the soaked grains, a trick that I find works well to incorporate the eggs thoroughly, too. After adding the remaining ingredients, I often switch to a whisk and mix the batter until there are very few lumps.
  • This muffin recipe could also be made into blueberry, cinnamon, lemon, etc.
  • I love using an ice cream scoop to scoop the batter into the muffin tins. It’s the perfect amount and comes out easily.
  • Active starter or discard will work for this recipe. I love making them into sourdough discard muffins by using up that extra discard.
  • If you want to use sugar rather than honey, simply use sugar and add at least 1/2 cup more of sourdough starter. If your starter is thicker, you may need a little more starter than 1/2 cup.

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How Do I Get A Sourdough Starter?

You can easily create your own sourdough starter. Learn how I make a quick and easy starter here that I’ve had for years.

You can also buy one from a local bakery, order them online, or ask a friend. 

Can I use sugar instead of honey?

Yes! Swap out the sugar for honey and add 1/2 cup extra sourdough starter. If your starter is on the thicker side, you may need to add a little more than 1/2 cup.

Do you have to long ferment this recipe?

No. You can totally just mix all the ingredients together and bake and it works just as well. You won’t be getting the benefit of the fermented grain though.


Sourdough starter: active or discard

All purpose flour – FYI you can find the best deal at Costco.

Butter: Unsalted butter. To make this dairy free, use coconut oil or avocado oil.

Honey: Substitute with maple syrup or even sugar. See recommendations for substitutions in the recipe card.


Baking soda


Vanilla extract: Homemade or store-bought

Chocolate chips: Mini chocolate chips are my favorite, but regular or even chocolate chunks will also work.

Tools you may need:

Muffin tin

Stand mixer with paddle attachment, hand mixer, or just a large bowl


Silicone spatula

Measuring cups (liquid and dry) and spoons

Ice cream scoop (optional, but really useful)

Muffin liners

Find More Sourdough Muffin Recipes:

sourdough muffin on a white plate with more muffins in the background on a wood cutting board

How To Make Long Fermented Sourdough Chocolate Chip Muffins

In a large bowl, mix together melted butter, honey, flour, and active sourdough starter.

The dough will be thick and will thicken as it ferments.

Depending on how hydrated your starter is, you may need to add a touch of water. I have a 100% hydration starter meaning I feed my starter equal parts water to flour.

Cover and allow to ferment for 12 to 24 hours at room temperature.

The next day preheat the oven to 375 degrees. 

Line muffin tins with cupcake liners or grease well.

Uncover the bowl of muffin batter that was fermenting and add vanilla extract, baking soda, eggs, and salt to the batter.

Start mixing all the ingredients together. That stand mixer with a paddle attachment makes this way easier and gives the best results.

I like to just use my hands to break up large clumps and really combine the eggs with the batter. It is natural for the batter to be pretty firm.

Once the batter starts coming together, add chocolate chips and use a whisk to whip it together and break up any more large lumps.

Spoon into muffin tins equally. 

Bake for 20-25 minutes until tops start turning golden brown and a toothpick comes out clean.

Flip onto a cooling rack and allow to cool. A plate works well, too.

sourdough muffins right from the oven in a muffin tin

Quick Sourdough Discard Chocolate Muffins:

Preheat the oven to 375 degrees F. Grease a muffin 12-cup muffin tin or add muffin liners.

In a stand mixer with paddle attachment, or large bowl, add oil and sugar. Mix well on medium speed.

Add remaining wet ingredients and mix: eggs, vanilla extract, and sourdough starter until well combined.

Mix in dry ingredients. Until combined. 

Fold in chocolate chips.

Spoon batter into each muffin well.

Bake for 20-25 minutes, or until the tops of the muffins start to turn golden and a toothpick comes out clean.

​Allow to cool for a few minutes and transfer to a wire rack.


sourdough muffin with a nite taken out on a white plate with chocolate chips


Place in an airtight container or storage bag and keep for three days. You can also freeze for up to three months.

Find More Family Favorite Sourdough Recipes:

Tried this recipe and loved it? I would love if you would come back and give it 5 stars. Please and thank you! Tag me on Instagram @ablossominglife.

overhead shot of sourdough chocolate chip muffins on a wood cutting board.

Sourdough Chocolate Chip Muffins

Delicious and soft chocolate chip sourdough muffins are a naturally sweetened and fermented snack
5 from 4 votes
Print Pin Rate
Author: Amy
Prep Time: 15 minutes
Cook Time: 20 minutes
Servings: 12 muffins



  • 1/2 cup sourdough starter active
  • 1.5 cups all purpose flour
  • 1/3 cup butter melted
  • 3/4 cup honey
  • 2 eggs
  • 3/4 tsp baking soda
  • 1/4 tsp salt
  • 1 tsp vanilla
  • 1/2 cup mini chocolate chips You could also use regular chocolate chips or chocolate chunks


  • In a large bowl or a bowl of a stand mixer, mix together melted butter, honey, flour, and sourdough starter.
  • Cover and allow to ferment for 12 to 24 hours. (optional)
  • The next day preheat oven to 375 degrees. Line muffin tins with muffin liners or grease well.
  • Add vanilla extract, baking soda, eggs, and salt to the fermented batter.
  • Start mixing all the ingredients together with the paddle attachment or a whisk.
  • Once the batter starts coming together, add chocolate chips, and mix. Breaking up any more large lumps.
  • Spoon into muffin tins equally. 
  • Bake for 20-25 minutes until tops start turning golden brown and a toothpick comes out clean.
  • Flip onto baking rack and allow to cool. A plate works well, too.


You can make this recipe without the long fermentation. Just mix all the ingredients together and bake. Still yummy.
The fermentation is just to help break down the phytic acid and some of the gluten making it easier to digest.
Substitute sugar for the honey. Add an extra 1/2 cup of sourdough starter for added moisture.


Serving: 1muffin | Calories: 225kcal | Carbohydrates: 37g | Protein: 3g | Fat: 8g | Saturated Fat: 5g | Polyunsaturated Fat: 0.4g | Monounsaturated Fat: 2g | Trans Fat: 0.2g | Cholesterol: 42mg | Sodium: 174mg | Potassium: 40mg | Fiber: 1g | Sugar: 22g | Vitamin A: 214IU | Vitamin C: 0.2mg | Calcium: 18mg | Iron: 1mg
Course: Breakfast, Dessert, Snack
Cuisine: American
Keyword: sourdough chocolate chip muffins, sourdough muffins
Tried this recipe? Tag me!Mention @ablossominglife or tag #ablossominglife!


  1. 5 stars
    I used my fresh milled hard red whole wheat flour, 12hr fermentation, whole family approved! Thank you!!!!

  2. hi, do you think you could mix this with a whisk after the fermentation? Do you think it would come together?

    1. I think you would need to break it up with your hands first then move to a whisk. I’ve done like this before.

  3. 5 stars
    Hi Amy,
    Can I know whether the dough can be fermented in fridge or at room temperature? My place is kind of hot, above 30 degree. Thank you

    1. It can be fermented at room temperature since it doesn’t include eggs until after the fermentation. If your house is very warm than it may not need to ferment as long.

  4. 5 stars
    Fantastic muffins! I did the 24 hour long ferment and my family could not even taste the sourdough. They were definitely easier to digest, no heavy or upset stomach after eating. Thank you so much for the recipe. I have made it several times and am finally printing it out so I can make it without having to get my phone for the recipe.

  5. 5 stars
    I have made this rebote twice, doubling it the second time around. Even though I am totally enamored with sourdough, my kids, not so much. But this recipe, my family loves. Each time I’ve made them, I’ve used raspberries, squeezing the juice of an orange per recipe. No-one could tell that this was a sourdough recipe!

  6. What about adding shredded zucchini after the fermentation, wondering if that might work? Looking forward to making these!

  7. So glad to find this long fermentation recipe for muffins! I make green smoothie muffin recipe where I mix the batter in a blender to combine the spinach? If I want to add spinach to this and blend in it properly, when would you suggest I add it? Or is this just a bad idea?? Thanks!

    1. Hmmm I think that would be a challenge. If you were doing the quick version and not fermenting I could see adding it. But because the batter becomes stiff during the fermentation it may be challenging.

  8. Why wouldnt you long ferment this recipe the same way you long ferment the chocolate chip cookie recipe. Would this ferment in the fridge for 48=72 hours the same way the cookie dough does? The cookies are excellent, by the way! Thanks!

    1. Yay! I’m glad you like them! Great question. The muffin batter is much wetter than the cookie dough, so in my mind I thought the cookie dough would be too stiff after leaving it out without the egg overnight and would be too hard to incorporate the egg after. You may be able to do it. Maybe I’ll try it so I have another reason to make more cookies 😂.

  9. I need the recipe for your sour dough bread..I have your sour dough starter but can’t find your recipe for the bread.

5 from 4 votes

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