Fermented sourdough chocolate cupcakes are a decadent and deliciously rich chocolate cake topped with cream cheese buttercream frosting. Great for a birthday celebration or a fun weekend dessert, the slight sourdough tang makes this recipe especially delicious.

sourdough chocolate cupcake with white frosting cut in half on a white and blue antique plate

The first time I made these sourdough cupcakes was for a special date night in with Luke. I lit candles, prepared a fancy dinner, and to top it off, we enjoyed this dessert at the end.

Itโ€™s truly the best way to finish up a date night. A light, fluffy, slightly tangy, but incredible rich chocolate cake covered in the best cream cheese buttercream frosting. Twist my arm. How could anyone resist? 

I love long fermentation. Iโ€™ve gone in depth on the blog, YouTube, and my podcast about how we utilize fermented grains and sourdough in our home. 

Creating sourdough recipes has become a passion of mine. Not just your run of the mill sourdough bread, but expanding it to include cookies, brownies, pumpkin rolls, cobbler, muffins, and much, much more. 

The fermentation process breaks down the phytic acid and gluten in the flour, making more of the nutrients available for your body to absorb, and easier for digestion.

Often, Iโ€™m asked what the key to sourdough is. And honestly, it is to just start and donโ€™t give up. So many people are on day five of creating their sourdough starter and itโ€™s still flat. They toss it and give up. 

Donโ€™t do that. Continue to feed it, and I promise you that you will have an active, wild yeast full product that you will be able to use to make so many yummy creations. The possibilities are endless.

sourdough cupcake with cream cheese buttercream frosting on a white and blue antique plate

Sourdough Chocolate Cupcake Tips:

  • If you are new to sourdough, check out how to create your own sourdough starter here.
  • Pinched for time? You can skip the overnight fermentation and just use sourdough discard.
  • Active sourdough starter or sourdough discard will work in this recipe. 
  • Coffee and chocolate go perfectly together in this recipe, giving it a richer, deeper chocolate flavor. 

This post contains affiliate links, which means I make a small commission at no extra cost to you. See my full disclosure here.

sourdough chocolate cupcake with white frosting on a antique stove with more cupcakes in the background

Tools:

Muffin tin

Stand mixer

Measuring cups and spoons

Ice cream scoop (optional, a dry measuring cup also works well)

sourdough chocolate cupcake with cream cheese buttercream frosting on a white and blue antique plate
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How To Make Sourdough Chocolate Cupcakes

The Day Before:

In a bowl, mix together the following ingredients just until combined: flour, sourdough starter, coconut oil, and water. Cover with a towel or plastic wrap and allow to sit overnight or up to 24 hours.

The Next Day:

women wearing a blue apron placing cupcake liner into muffin tin wells

Preheat the oven to 350ยบ F and line or grease muffin tins.

In a large bowl, mix together sucanat or rapadura (regular sugar would work, as well), salt, and finely ground coffee (optional).

To the dry ingredients, add eggs, vanilla, cocoa powder, and whole milk. 

sourdough chocolate cupcake batter in a large bowl next to muffin tins filled with liners

Next, add the sourdough mixture into the egg, sugar, and milk mixture. Whisk to incorporate until smooth. I like to make this in the stand mixer, because it is so much easier to incorporate.

Lastly, sprinkle in baking soda and mix well.

women wearing a blue stripped apron pouring sourdough cupcake batter into lined muffin tins

Add equal amounts of sourdough cupcake batter to each well. I love using an ice cream scoop for this, a measuring cup also works well.

Bake for 15-20 minutes, until a toothpick inserted comes out clean. 

Remove from the oven. Allow to cool for about 10 minutes, then remove the cupcakes and allow them to cool completely on a wire rack before frosting.

sourdough cupcake with cream cheese buttercream frosting on a blue and white antique plate with a spoon

Make The Cream Cheese Frosting:

In a large bowl or stand mixer, add room temperature butter and cream cheese.

Cream together with a whisk attachment until well combined.

Add vanilla and salt. 

On slow speed, slowly add powdered sugar. 

Once the sugar is added, turn speed to medium and allow the frosting to become nice and fluffy.

Place into a piping bag (or just place in a large ziplock back and snip the corner off) and pipe onto the cupcakes. 

Decorate with chocolate chips, sprinkles, strawberries, etc.

Find More Delicious Sourdough Desserts:

If you try this recipe and love it, I would love if you could come back and give it 5 stars! Tag me on Instagram @farmhouseonboone

Sourdough Chocolate Cupcakes

4.41 from 89 votes
Great for a birthday celebration or a fun weekend dessert, these sourdough chocolate cupcakes are absolutely delicious and will become your go-to chocolate cake recipe.
Prep: 10 minutes
Cook: 15 minutes
Additional Time: 12 hours
Total: 12 hours 25 minutes
Servings: 24 cupcakes
close up picture of a sourdough cupcake with white frosting on an white antique stove
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Ingredients 

  • 2 cups flour
  • 1/2 cup coconut oil
  • 1/2 cup sourdough starter
  • 1 cup water
  • 2 large eggs
  • 2 cups sucanat or rapadura, regular sugar would also work
  • 1 teaspoon salt
  • 1 teaspoon finely ground coffee, optional
  • 2 teaspoons vanilla
  • 3/4 cup cocoa
  • 1 cup whole milk
  • 2 teaspoons baking soda

Frosting

  • 1/2 cup butter, room temp
  • 8 ounces cream cheese, room temp
  • 2 teaspoons vanilla
  • 1/4 teaspoon salt
  • 4 cups powdered sugar

Instructions 

  • In a bowl, mix together the following ingredients just until combined: flour, sourdough starter, coconut oil, and water.
  • Cover with a towel or plastic wrap and allow to sit overnight or up to 24 hours.

The next day:

  • Preheat the oven to 350ยบ F. In a large bowl, mix together sucanat or rapadura, salt, and finely ground coffee (optional).
  • To the dry ingredients, add eggs, vanilla, cocoa powder, and whole milk. Next, add the sourdough mixture into the egg, sugar, and milk mixture. Whisk to incorporate until smooth.
  • Lastly, sprinkle in baking soda and mix well.
  • Grease or line muffin tin, then add equal amounts of sourdough cupcake batter to each well. Bake for 15-20 minutes, until a toothpick inserted comes out clean. Remove from the oven. Allow to cool for about 10 minutes, then remove the cupcakes and allow them to cool completely before frosting.

Make Frosting:

  • In a large bowl or stand mixer, add room temperature butter and cream cheese.
  • Cream together with a whisk attachment until well combined.Add vanilla and salt. On slow speed, slowly add powdered sugar. Once the sugar is added, turn speed to medium and allow the frosting to become nice and fluffy.
  • Place into a bag for piping and pipe onto the cupcakes. Decorate with chocolate chips, sprinkles, strawberries, etc.

Notes

  • You can use active sourdough starter or sourdough discard.
  • Ferment this recipe for more health benefits or just mix it up and bake without fermenting.

Nutrition

Serving: 1cupcake | Calories: 312kcal | Carbohydrates: 48g | Protein: 3g | Fat: 13g | Saturated Fat: 9g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 0.2g | Cholesterol: 36mg | Sodium: 284mg | Potassium: 94mg | Fiber: 1g | Sugar: 37g | Vitamin A: 284IU | Calcium: 33mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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4.41 from 89 votes (86 ratings without comment)

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63 Comments

  1. Angie says:

    I was going to make 2 batches for 2 different parties however One party was postponed. I already have completed 1& 2 in the instructions. Is there another flavor I can use this on.

    1. Lisa Bass says:

      You could always frost one with chocolate icing and the other with vanilla icing!

  2. Paige says:

    5 stars
    Absolutely love this recipe! I make it for all my kids birthday parties!
    How can I make these vanilla?

    1. Lisa Bass says:

      The cocoa powder can be substituted for all purpose flour. I like to add a little extra vanilla extract to my vanilla cakes.

  3. Erin B says:

    My cupcakes turned out really dense. Any chance you know why that would happen?

    1. Lisa Bass says:

      It can actually be caused by a variety of things! Your oven temperature, over mixing the dry ingredients, or a wrong flour measurement could cause them to be more dense.

  4. Heather says:

    These cupcakes were the absolute best – thank you for the recipe!

  5. jenna says:

    I stirred together the initial ingredients and let it sit overnight. Then didn’t have time to finish so I stuck the mixture in the fridge for a couple days…long ferment…. Do you think it will still turn out okay?

  6. Herb Davis says:

    I first tried the cake, and it turned out fantastic. I made German Chocolate icing for the cake, and everyone loved it. I double checked the recipe and noticed it’s exactly the same and the same for these. I also added Raspberry preserves to each layer of the cake before the icing. It was great. I will use your frosting recipe for the next batch. But for now, I will keep on trying new things, thanks for all your recipes and ideas.

  7. Keiki says:

    Can you make this into a cake instead of cupcakes?
    Just dividing the batter or do you think it will be to thin of a cake?

    1. Kat says:

      5 stars
      Hi! Is the coconut oil in solid or liquid(melted) form? Escorted to make these for my daughter’s birthday!

      1. Lisa Bass says:

        Melted!

  8. Kealey says:

    Do you allow the first mixture to sit on the counter overnight or the fridge?

    1. Lisa Bass says:

      I let it sit on the counter over night.

  9. Nicole says:

    Do you let it sit 24 hours out on the counter or fridge? I have little sugar ants that may get in to it on the counter overnight.

    1. Lisa Bass says:

      You can let these sit in the fridge over night.

  10. Elsa says:

    Just made these tonight and they were a hit! Very yummy and moist! Thanks for the recipe, Iโ€™ll definitely add it to my favorites.

    1. Lisa Bass says:

      Glad you enjoyed it! These are a family favorite too.