What if we told you your sourdough discard could be the secret ingredient to the most decadent, moist, chocolate-packed muffins you’ve ever baked? These Sourdough Discard Double Chocolate Yogurt Muffins are rich, fluffy, and irresistibly fudgy. Plus, it‘s the perfect way to use up sourdough discard, milk and yogurt!

This recipe is incredibly simple, using simple ingredients, and sure to be a hit with the family. My kids beg me to make them constantly. An added bonus - real ingredients you can feel good about!
Check out other super simple sourdough discard recipes, such as my Sourdough Discard Banana Bread here or the best Fluffy Sourdough Discard Waffles here. For more sourdough muffin recipes try out my Sourdough discard Pumpkin Muffins here or my super simple Discard Apple Muffins here.
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Learn to make your own yogurt following my super simple step by step guide here.
Ingredients
The most delicious way to use up sourdough discard, yogurt, and milk! Add just a few more ingredients and you have the tastiest double chocolate muffins.

Dry Ingredients
- All Purpose Flour
- Cup Sugar
- Cup Cocoa Powder
- Baking Soda
- Baking Powder
- Salt
Wet Ingredients
- Eggs
- Plain Greek Yogurt
- Olive Oil
- Milk (sour raw milk)
- Sourdough Discard (or active starter)
- Vanilla Extract
Mix In Ingredients
- Chocolate Chips
See recipe card for quantities.
Instructions
First, preheat oven to 350 degrees. Grease a muffin tin or line a muffin pan with paper liners or muffin cups.
Combine all wet ingredients and mix well. Add in all dry ingredients to the wet batter and mix until there is a smooth muffin batter, I like to use my stand mixer.

Fold in the chocolate chips until they’re evenly distributed into the sourdough chocolate muffin batter.

Add the batter to the muffin tins, filling about ⅔ full. Once the oven temperature reaches 350 degrees, place the muffin tins into the preheated oven and bake the double chocolate sourdough muffins for 25 minutes. Check to ensure the muffins are done by inserting a toothpick into the center of a muffin. It should be clean when removed, if not bake for a bit longer.

Allow the muffins to cool for about 5-10 minutes on a cooling rack. Finally, enjoy the rich chocolate flavor of the double chocolate muffins!

Substitutions
Try these ingredient substitutions:
- Milk - this recipe is a great way to use up sour milk or buttermilk, but regular whole milk works well too
- Yogurt - I like to use up homemade yogurt in this recipe, but sour cream works well as a substitute
- Olive Oil - coconut oil is a great substitute for olive oil if necessary
- Sourdough Discard - active sourdough starter works as well, but this recipe is a delicious way to use up discard
Equipment
- Muffin Tin
- Mixing Bowl
- Muffin Liners
- Spatula
- Toothpick
- Stand Mixer (optional)

Storage
Store in an airtight container or covered in plastic wrap. Muffins will keep on the counter, if they last that long around chocolate lovers.
FAQ
Sour cream is a great substitution for yogurt.
Yes, active sourdough starter can be used instead of discard.
I have not tried this recipe using alternative milk options. However, sour milk, buttermilk, raw milk, and whole milk all work great.
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Sourdough Discard Double Chocolate Yogurt Muffins
Equipment
- Large Bowl
- Stand Mixer or Hand Mixer
- Muffin Tin
Ingredients
Dry Ingredients
- 2 Cups All Purpose Flour
- 1 Cup Sugar
- ½ Cup Cocoa Powder
- 1 teaspoon Baking Soda
- ½ teaspoon Baking Powder
- ½ teaspoon Salt
Wet Ingredients
- 2 Eggs
- ⅔ Cups Plain Greek Yogurt
- ½ Cups Olive Oil
- ⅓ Cup Milk sour
- ⅓ Cup Sourdough Discard or active starter
- 2 teaspoons Vanilla Extract
Mix In Ingredients
- 2 Cups Chocolate Chips
Instructions
- First, preheat oven to 350 degrees. Grease a muffin tin or line a muffin pan with paper liners or muffin cups.
- Next, combine all wet ingredients. Mix well.
- Add in all dry ingredients to the wet batter and mix until there is a smooth muffin batter, I like to use my stand mixer.
- Fold in the chocolate chips until they’re evenly distributed into the sourdough chocolate muffin batter.
- Add the batter to the muffin tins, filling about ⅔ full. Once the oven temperature reaches 350 degrees, place the muffin tins into the preheated oven and bake the double chocolate sourdough muffins for 25 minutes.
- Check to ensure the muffins are done by inserting a toothpick into the center of a muffin. It should be clean when removed, if not bake for a bit longer.
- Allow the muffins to cool for about 5-10 minutes on a cooling rack. Finally, enjoy the rich chocolate flavor of the double chocolate muffins!
Notes
- Milk - this recipe is a great way to use up sour milk or buttermilk, but regular whole milk works well too
- Yogurt - I like to use up homemade yogurt in this recipe, but sour cream works well as a substitute
- Olive Oil - coconut oil is a great substitute for olive oil if necessary
- Sourdough Discard - active sourdough starter works as well, but this recipe is a delicious way to use up discard
Nutrition
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Laura says
Thank you for sharing this wonderful recipe! What a treat for a weekend breakfast!
Rebecca says
These muffins sound yummy! Can’t wait to bake these for my kids
Megan says
Love that this calls for Greek Yogurt. I've been trying to incorporate it into more of my meals but I'm getting tired of smoothies! 🙂
Heidi says
What a wonderful recipe! I love that it uses sourdough and sour milk. Great way to use up both, double chocolate always gets my attention. Love this!
Kirsten says
Yum! We’ve been on a muffin kick lately, so we’ll definitely be saving these for later!
Emily says
These look so amazing! Can't wait to try them out 🙂