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Home » Fresh Milled Flour Recipes

Sourdough Chocolate Cupcakes (with fresh milled flour)

Published: Mar 13, 2025 · Modified: Mar 26, 2025 by Parker · This post may contain affiliate links · Leave a Comment

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If you’re looking for a rich, moist, and deeply chocolatey dessert that the whole family will devour, these sourdough chocolate cupcakes are it! Made with fresh-milled soft white wheat and spelt flour, this recipe has the perfect balance of indulgence and nourishment.  

These cupcakes are naturally fermented with sourdough starter, giving them a depth of flavor that makes them even more special. And since they contain no artificial dyes, they make a festive and wholesome treat for St. Patrick’s Day—or any day you’re craving chocolate

Ingredients to make sourdough chocolate muffins

Why You’ll Love These Fresh-Milled Flour Sourdough Chocolate Cupcakes  

  • Naturally fermented – The sourdough starter adds a subtle tang and enhances the chocolate flavor.  
  • Soft, fluffy, and rich – Thanks to fresh-milled flour, buttermilk, and coconut oil, these cupcakes are ultra-moist.  
  • Toddler-tested & approved– If my little one can make these, so can you!  
  • No artificial colors – A perfect St. Patrick’s Day treat without the need for synthetic food dyes.  

Equipment Needed:

  • Food Processor
  • Grain Mill
  • Mixer
  • Measuring cups, spoons, and kitchen scale
Sourdough Chocolate cupcakes with homemade pistachio buttercream

Ingredients for the Best Sourdough Chocolate Cupcakes  

  • 120 grams soft white flour (freshly milled)  
  • 120 grams spelt flour (freshly milled)  
  • ½ cup coconut oil, melted and cooled  
  • ¾ cup sourdough starter  
  • ½ cup water  
  • 2 large eggs  
  • 2 cups sugar  
  • 1 teaspoon salt  
  • 1 tablespoon vanilla  
  • ¾ cup cocoa powder  
  • 1 cup buttermilk  
  • 2 teaspoons baking soda  

If you love Sourdough Chocolate Cupcakes, you may also like:

  • Fresh Milled Flour Sourdough Chocolate Chip Cookies
  • Homemade Cookie Dough Granola
  • Fresh Milled Flour Sourdough Waffles

Instructions

Preheat and Prepare

Preheat the to 350 degrees, line the muffin tin with liners, and mill your flour.

Mixing the wet ingredients

Mix the wet ingredients (except the buttercream)

 In a large bowl, whisk together the melted coconut oil, sourdough starter, water, eggs, sugar, and vanilla. Mix until combined and smooth

Mix the dry ingredients

In a separate bowl, sift together the fresh-milled flours, cocoa powder, salt, and baking soda.

Add the dry ingredients and buttermilk

Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Be careful not to overmix. Then add in the buttercream slowly.

Bake

Divide the batter evenly among the cupcake liners, filling each about ¾ full. Bake for 18-22 minutes or until a toothpick inserted in the center comes out clean.  

Enjoy!

Let the cupcakes cool in the pan for 5 minutes before transferring to a wire rack to cool completely.  Ice with my favorite pistachio buttercream and enjoy.

Sourdough Chocolate cupcakes with homemade pistachio buttercream

Sourdough Chocolate Cupcakes (with fresh milled flour)

Parker
Made with tangy sourdough and fresh milled flour, these rich, tender, and delicious cupcakes are perfect for any occasion.
Print Recipe Pin Recipe
Prep Time 10 minutes mins
Cook Time 10 minutes mins
Course Dessert
Servings 19

Equipment

  • 1 Grain Mill
  • 1 Kitchen Aid
  • 1 Food Processor
  • Measuring cups and spoons
  • Mixing Bowls

Ingredients
  

  • 120 grams soft white flour freshly milled
  • 120 grams spelt flour freshly milled
  • ½ cup coconut oil melted and cooled
  • ¾ cup sourdough starter
  • ½ cup water
  • 2 large eggs
  • 2 cup sugar
  • 1 teaspoon salt
  • 1 TBS vanilla
  • ¾ Cup ¾ cup cocoa powder
  • 1 cup buttermilk
  • 2 teaspoon baking soda

Instructions
 

  • Preheat & Prep
  • Preheat your oven to 350°F (175°C). Line a muffin tin with cupcake liners
  • Mix the wet ingredients
  • In a large bowl, whisk together the melted coconut oil, sourdough starter, water, eggs, sugar, and vanilla until well combined.
  • Combine dry ingredients
  • In a separate bowl, sift together the fresh-milled flours, cocoa powder, salt, and baking soda.
  • Mix the batter
  • Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Be careful not to overmix! Next slowly add the buttermilk until combined.
  • Fill the cupcake liners and bake
  • Divide the batter evenly among the cupcake liners, filling each about ¾ full. Bake for 18-22 minutes or until a toothpick inserted in the center comes out clean.
  • Cool & Enjoy
  • Let the cupcakes cool in the pan for 5 minutes before transferring to a wire rack to cool completely

Notes

Store in an airtight container for 2-3 days. 
 
You can use active starter or discard.
Keyword Sourdough Chococlate Muffins

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  • Why I Started Milling My Own Flour
  • Fresh Milled Flour Easter Blondies
  • Fresh Milled Flour Sourdough Cadbury Egg Cookies

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Hey, I'm Parker

Welcome! I’m so excited you’re here. Let’s roll up our sleeves and get cooking and baking from scratch to nourish our families with love and deliciousness. Can’t wait to share all the recipes with you!

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