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Home » All Recipes

Sourdough Chocolate Cupcakes

Updated: Jul 20, 2025 · Published: Mar 26, 2025 by Audrey · This post may contain affiliate links · 2 Comments

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My sourdough chocolate cupcakes are rich, moist, and full of sourdough goodness. I made these for my son's third birthday (see excited toddler cake tester hand in the picture below) and they were a hit!

The sourdough discard adds a subtle depth to the chocolate flavor that can't be beat. On top of that, these cupcakes are a great way to use up ⅓ cup of your extra sourdough discard if you have it on hand. Add this recipe to your list for your next special occasion!

Overhead picture of sourdough discard chocolate cupcakes with sprinkles, chocolate shavings, and a toddler's hand reaching for them.

If you are looking for long-fermented sourdough cupcakes, you're in luck! Scroll to my "Variations" section below for step-by-step instructions on how to long ferment them.

One of the reasons I was so excited about this recipe is how versatile it can be and how chocolate cupcakes are a welcome treat for any special occasion (or even just on a regular Tuesday). Make these for birthday parties like I did, add festive sprinkles and liners for Christmas, Valentine's Day, Easter, Independence Day, and more. You can make these totally your own!

If you are looking for more cupcake recipes, try out my strawberry crunch cupcakes and my cinnamon matcha cupcakes. If sourdough discard recipes are more your speed, check out my other sourdough recipes.

If you try this recipe please let me know what you think!

Jump to:
  • Ingredients
  • Instructions
  • Substitutions
  • Variations
  • Equipment
  • Storage
  • Top tip
  • FAQ
  • Related
  • Sourdough Chocolate Cupcakes

Ingredients

This recipe uses simple ingredients that are easy to find so you can whip these up any time you want them!

Overhead, labled picture of the ingredients needed to make sourdough chocolate cupcakes.

For the sourdough chocolate cupcakes:

  • All purpose flour
  • Cocoa powder
  • Baking soda
  • Baking powder
  • Salt
  • Large eggs
  • Sourdough discard (active sourdough starter works too)
  • Oil (vegetable oil or coconut oil)
  • Milk
  • Vanilla extract
  • Sugar
  • Brown sugar

For the chocolate frosting (not pictured in the above ingredient photo):

  • Butter (Salted or unsalted butter works fine)
  • Powdered sugar
  • Cocoa Powder
  • Vanilla extract
  • Milk
  • Sprinkles (I like these dye-free ones)

See recipe card for quantities.

Instructions

Step 1 of instructions for sourdough chocolate cupcakes. Overhead picture of separated wet and dry ingredients.

Step 1: Preheat your oven to 350°F and prepare your muffin tin with cupcake liners.

Mix the wet and dry ingredients separately.

Step 2 of instructions for sourdough chocolate cupcakes. Overhead picture of finished chocolate cake batter.

Step 2: In a large mixing bowl or bowl of a stand mixer with a paddle attachment, slowly add the wet ingredients into the dry ingredients, stirring carefully so as not to overmix the batter. (Overmixing can cause sinking or overly dense cupcakes.)

Step 3 of instructions for sourdough chocolate cupcakes. Overhead picture of chocolate cupcake batter in 12 muffin liners.

Step 3: Use a 3-tablespoon cookie scoop to evenly divide the batter between 14 cupcake liners. It will be about ¾ of the way full.

Bake cupcakes for 18-20 minutes at 350°F. 18 minutes is perfect for me! They are done when the tops are set and a toothpick inserted in the center comes out clean.

Step 4 of instructions for sourdough chocolate cupcakes. Overhead picture of chocolate cupcakes with chocolate buttercream.

Step 4: Allow the cupcakes to cool completely on a wire rack.

Make the buttercream using a whisk attachment (or paddle) and decorate to your heart's content!

Note: If you cupcakes aren't cooled completely by the time you are done making your frosting, cover the bowl with plastic wrap and leave it at room temperature until the cupcakes are nice and cool.

Hint: Use a flour sifter to add the powdered sugar and cocoa powder to the buttercream to ensure a smooth, easy-to-pipe frosting.

Substitutions

If some of the ingredients don't work for you, that's totally fine!! Here are some of my recommended substitution ingredients. 

  • Milk: Use high-fat non-dairy milk if you don't want to use dairy! I highly recommend  Oatly oat milk (full-fat or regular would be ideal).
  • Butter: Use a non-dairy butter like Country Crock's plant butter. I've also had great luck using that brand in frosting.

Variations

This recipe can be easily switched up to create new and interesting flavors. Here are some fun ideas to try out!

  • Espresso: Add a teaspoon of instant espresso powder with your flour for the cupcakes or with the powdered sugar in the buttercream.
  • Toppings: Top with berries, oranges, chocolate curls, sprinkles, or Oreo cookie crumbles. For holidays, use festive sprinkles!
  • Buttercream: You can swap this recipe for vanilla buttercream or try something a bit more fun like the strawberry buttercream frosting in my strawberry crunch cupcake recipe. You can make it without the "crunch" if you'd prefer!
  • Long-fermented: Mix flour, milk, sourdough starter, and oil in a bowl. Cover and store in your fridge for 24 hours. Alternatively, you can leave it at room temperature overnight to ferment, as the bacteria in the starter will prevent the milk from spoiling. The next day, add the remaining ingredients and bake from there!
  • Double chocolate: Add ¾ cup of chocolate chips to the cupcake batter before baking. The same amount of walnuts would be delicious too!

Equipment

  • Kitchen scale (please weigh your ingredients)
  • Stand mixer (or large mixing bowl with an electric mixer)
  • Medium bowl
  • Muffin tin or cupcake tin
  • Paper liners
  • Three tablespoon cookie scoop (optional)
  • Flour sifter (optional)
  • Piping bag (optional)
  • Icing tip of choice (optional)
  • Peeler

Storage

Store in an airtight container in the refrigerator for up to 4 days. Can be frozen for up to 3-6 months, preferably without frosting (however, I've frozen and thawed decorated cupcakes in the refrigerator, and they were still delicious.)

Top tip

Weigh your ingredients! I can't recommend this enough. Kitchen scales are easy to find, affordable, and beneficial to your baking journey. It is the best way to make sure your recipes turn out as accurate as possible. See my "equipment" section above for links to scales I recommend.

FAQ

Can I make dairy-free sourdough chocolate cupcakes?

Absolutely! Check out my "substitutions" section above for my favorite dairy alternatives for baking.

Related

Looking for other sourdough recipes like this? Try these:

  • Picture of a hand holding chocolate cinnamon rolls with cinnamon espresso cream cheese frosting with more cinnamon rolls in the background.
    Chocolate Cinnamon Rolls with Cinnamon Espresso Cream Cheese Icing
  • Picture of chocolate peppermint kiss cookies stacked on each other. Chocolate cookies rolled in sugar with a Hershey's peppermint kiss in the center.
    Chocolate Peppermint Kiss Cookies
  • Overhead picture of sourdough gingerbread cookies.
    Chewy Sourdough Gingerbread Cookies
  • Overhead picture of chocolate sour cream pound cake cupcakes.
    Chocolate Sour Cream Pound Cake Cupcakes
Picture of sourdough discard chocolate cupcakes with rainbow sprinkles and chocolate curls.

Sourdough Chocolate Cupcakes

Audrey
These sourdough chocolate cupcakes are rich, soft, and delightfully sweet with a balanced tang from the sourdough discard. Topped with a simple chocolate buttercream, these cupcakes are perfect for any occasion.
Print Recipe Pin Recipe
Prep Time 15 minutes mins
Cook Time 18 minutes mins
Course Dessert
Cuisine American
Servings 14 Cupcakes

Equipment

  • Food scale
  • Stand Mixer (or large mixing bowl and whisk)
  • Medium bowl
  • Muffin/cupcake pan
  • Cupcake liners
  • Three tablespoon cookie scoop (optional)
  • Flour sifter (optional)
  • Piping bag (optional)
  • Icing tip of choice (optional)
  • Potato peeler (optional, for chocolate shavings)

Ingredients
  

Sourdough Chocolate Cupcakes

  • ¾ cup all-purpose flour 90g
  • ½ cup cocoa powder 45g
  • 1 teaspoon baking powder
  • ¾ teaspoon baking soda
  • ¼ teaspoon salt
  • 2 eggs room temperature
  • ⅓ cup sourdough discard 100g
  • ½ cup cane sugar 100g
  • ½ cup brown sugar 100g
  • ⅓ cup vegetable oil 79ml
  • 2 teaspoons of vanilla extract
  • ½ cup milk 118 ml

Chocolate Buttercream

  • 1 cup salted butter softened, 227g
  • ½ cup cocoa powder 45g
  • 3 ½ cups powdered sugar 420g
  • 3 tablespoons milk
  • 2 teaspoons vanilla extract

Instructions
 

Sourdough Chocolate Cupcakes

  • Preheat your oven to 350F and prepare your cupcake pan with liners. If you want to ferment your batter, see the notes below for the instructions you'll need a day in advance.
  • In a large mixing bowl, mix your dry ingredients together. Set aside.
    ¾ cup all-purpose flour, ½ cup cocoa powder, 1 teaspoon baking powder, ¾ teaspoon baking soda, ¼ teaspoon salt
  • In a medium bowl, mix together your wet ingredients. Slowly mix your wet ingredients into your bowl of dry ingredients until just combined. The batter will be thin; Do not over mix!
    2 eggs, ⅓ cup sourdough discard, ½ cup cane sugar, ½ cup brown sugar, ⅓ cup vegetable oil, 2 teaspoons of vanilla extract, ½ cup milk
  • Use a three-tablespoon cookie scoop to evenly divide the batter between 14 cupcake liners. If you don't have a scoop like this, aim for ½-3/4 full in the liners.
    If you only have a 12-cupcake pan, it is fine to set the remaining batter aside while the first 12 bake.
  • Bake the cupcakes for 18-20 minutes at 350F until a toothpick inserted in the center comes out clean. 18 minutes is perfect for me, typically. Allow to cool completely before decorating.

Chocolate Buttercream

  • With a stand mixer and paddle attachment (or mixing bowl with a handheld mixer), beat the softened butter and vanilla until smooth and creamy. Scrape the sides of the bowl.
    In a medium bowl, whisk together cocoa powder and powdered sugar. Slowly add the sugar mixture to the butter (if the sugar or cocoa is clumpy, use a sifter to add it in to ensure a smooth result). Slowly add in the 3 tablespoons of milk until you achieve your desired consistency.
    1 cup salted butter, 3 ½ cups powdered sugar, 3 tablespoons milk, 2 teaspoons vanilla extract
  • Decorate your cooled cupcakes with the chocolate buttercream using a piping bag and icing tip (I used a Wilton 1M star tip) or even just a spoon or knife. Top with chocolate shavings* and/or sprinkles.

Notes

Long fermentation: Mix flour, milk, sourdough starter, and oil in a bowl. Cover and store in your fridge for 24 hours. Alternatively, you can leave it at room temperature overnight to ferment, as the bacteria in the starter will prevent the milk from spoiling. The next day, add the remaining ingredients and bake from there!
Salted butter in buttercream: I prefer salted butter in my buttercreams, but if you'd rather use unsalted, just add a pinch of salt to the buttercream. If using dairy free butter, don't add salt as they are usually well salted. 
Storage: Store at in the refrigerator for up to 4 days in an airtight container.
Chocolate shavings: To make chocolate shavings/curls, run a potato peeler along a chocolate bar. 
Keyword chocolate, cupcakes

More All Recipes

  • Overhead picture of brown butter sugar cookies stacked on top of each other.
    Brown Butter Sugar Cookies
  • Overhead picture of a hand holding a sourdough chocolate crinkle cookie with more cookies in the background.
    Sourdough Chocolate Crinkle Cookies
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Comments

  1. Kaitlyn says

    July 20, 2025 at 8:24 am

    Hi, cake portion is amazing! How much cocoa powder for the frosting? I’ve looked on the recipe and can’t seem to find, would love to complete these cupcakes 🩷

    Reply
    • Audrey says

      July 20, 2025 at 7:21 pm

      Hi Kaitlyn! I'm so sorry, it would be 1/2 a cup or 45 grams of cocoa powder! Updating the recipe now ❤️

      Reply

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Picture of Kneaded That Author Audrey Hawkins Grubb.

Hi, I'm Audrey! I’m a self-taught baker, mother of two boys, and a lifelong artist. I started baking regularly in 2020 and fell in love with creating sourdough discard recipes, breads, cookies, and cakes. A few years later, this blog grew from the lonely chaos of my husband’s first deployment, and now it’s where I get to share my recipes! You'll find a pretty even split between sourdough discard recipes and non-sourdough recipes, so there should be something for everyone!

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