Double Chocolate Sourdough Muffins with Fresh Milled Flour

These double chocolate sourdough muffins made with fresh milled flour are rich, fudgy, and wholesome — the perfect mix of bakery-style indulgence and the nourishing benefits of baking with whole grains. This easy small-batch recipe uses simple ingredients, real cocoa, and sourdough discard for incredible depth and a gorgeous tender crumb.

And if you’ve been hanging out with me here for a while, you already know: once I started using fresh milled flour, I never looked back. The flavor, the texture, the nutrition — it’s on a whole different level.

Milling my soft white wheat at home and baking with the flour warm and alive has changed the way I make breads, cakes, and muffins. There’s just something incredibly satisfying about turning white wheat berries into your own flour, using it right away, and tasting that richer flavor and subtle tang the very next day in something as simple as muffins.

These double chocolate sourdough muffins are one of my favorite sourdough recipes right now — Rich, chocolatey muffins that still feel wholesome enough for breakfast? Yes, please.

These double chocolate sourdough muffins use fresh milled flour for depth and nutrition, while sourdough discard adds just the right texture and flavor. They’re simple to mix, perfectly tender, and a delicious way to make the most of your sourdough starter — no fancy steps required.

They come together fast, require just two bowls, and they’re a great way to use up leftover sourdough discard that might otherwise sit in the fridge wrapped in plastic wrap.

Whether you’re new to baking with fresh milled flour, or already using a grain mill regularly, this is an easy recipe that gives you such a delicious end result without any fancy steps.

What You’ll Love About This Recipe

Here’s why these double chocolate sourdough muffins deserve a spot in your rotation:

• A great way to use sourdough discard. No need for an active sourdough starter — sourdough starter discard works perfectly here and adds amazing texture.
• Fresh milled flour gives them a richer flavor. Using whole grain flour from home-milled wheat berries adds a nutty flavor and fluffy yet soft texture you just don’t get with store-bought flour.
• Chocolate + chocolate. Cocoa powder plus a full cup of chocolate chips makes these feel like a treat while still being nourishing enough for breakfast.
• Simple ingredients. Everything comes together in one large mixing bowl, one separate bowl, and a standard muffin tin.
• Easy to store. You can store muffins in an airtight container for longer storage, and they stay moist and fudgy.

If you’ve ever made my sourdough apple muffins, sourdough pumpkin muffins, sourdough blueberry muffins, or sourdough banana muffins, then you know I love a good small-batch muffin recipe that uses real food ingredients without a lot of fuss.

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Key Ingredients

Here are a few highlighted ingredients: 

• Fresh milled flour–I use 2¼ cups freshly milled soft white wheat, though hard white wheat or hard red wheat will also work if that’s what you mill at home.
• Cocoa powder for that deep chocolate flavor.
• Sourdough discard — adds moisture, a little tang, and helps with rise.
• Chocolate chips — fold them right in for those melty pockets throughout.

I love that this recipe uses simple ingredients I already keep in my kitchen — the same ones I use for sourdough bread, english muffins, and most of my cakes and desserts.

You can find a full list of ingredients in the recipe card located at the bottom of this post.

How to Make Double Chocolate Sourdough Muffins with Fresh Milled Flour

Let me give you the process for making these deliciously simple muffins. 

Preheat the Oven—Heat your oven to 400°F. Line your muffin pan with muffin liners or lightly grease each cup. Starting with a hot oven helps create those high muffin domes we all love.

Mix the Dry Ingredients—In a large bowl, whisk together your dry ingredients: freshly milled flour, cocoa powder, salt, baking soda, and baking powder. This step ensures everything is evenly distributed and gives you the best rise.

Fresh milled flour behaves differently than store-bought flour because it still contains all parts of the wheat berry, so whisking well is important.

Mix the Wet Ingredients—In a separate bowl, whisk together your wet ingredients: sourdough discard, oil, egg, sweetener of choice, buttermilk, and vanilla extract. Make sure everything is at room temperature for the smoothest batter.

Combine the Batter—Pour the wet ingredients into the dry ingredients and stir gently with a spatula. Don’t overmix here — the batter should be thick. This is what gives the muffins their tall rise and tender crumb.

You don’t need a stand mixer for this one — hand mixing works perfectly.

Fold in Chocolate Chips—Add your chocolate chips and fold gently. This is where you can also swap in chopped dark chocolate, but I personally love the classic cup of chocolate chips.

Bake—Scoop the batter into your prepared muffin tin, filling each cup nearly to the top. This helps form those tall bakery-style tops that look like they came from your favorite grocery store bakery or an english muffin recipe but taste even better.

Bake for about 15 minutes. The tops should be set, and a toothpick inserted in the center should come out clean or with a few moist crumbs.

Cool + Serve—Let the muffins rest in the pan for 5 minutes before transferring them to a cooling rack. Serve warm if you want that melty chocolate moment — truly the best part.

Once cooled, you can store leftovers in an airtight container on the counter, or freeze them for longer storage. They reheat beautifully.

Baking Tips & Variations

• Honey vs sugar. You can use honey, white sugar, raw sugar, or brown sugar — all work with fresh milled flour.
• Try different wheats. Soft white wheat gives a tender crumb, but hard white wheat or red wheat berries add a slightly heartier, nuttier flavor.
• Add-ins. Fold in walnuts, raspberries, or chopped dark chocolate.
• Use discard or active starter. Active sourdough starter or discard both work, though discard gives a slightly more pronounced subtle tang.
• Make them your own. Use melted coconut oil, melted butter, or keep them classic with your favorite liquid oil.
• Flavor variations. Add lemon zest, swirl in sour cream, or turn this into a base for easy banana chocolate chip muffins with overripe bananas.

Recipe FAQs

More Fresh Milled Flour Recipes

If you’re loving baking with fresh milled flour as much as I am, here are some favorites:

• Whole Wheat Sourdough Bread
• Banana Bread using Fresh Milled Flour
• Fresh Milled Basic Muffins with Endless Variations

I love sharing how simple it can be to use your own sourdough starter and fresh milled flour your every day baking. Be sure to grab my Quick Start Guide to learn more about using fresh milled flour! I hope it will give you confidence and help you grow. I also have a course to walk you through using sourdough and fresh milled flour.

I hope these double chocolate sourdough muffins inspire you to pull out your grain mill, grab your sourdough discard, and enjoy just how simple and nourishing baking with fresh milled flour can be.

It’s recipes like this that remind me why I fell in love with the process in the first place — the flavor, the texture, the health benefits, and honestly just the joy of turning whole grains into something warm and homemade for my family.

And if you’re wanting to learn more about milling your own flour, don’t forget to grab my Quick Start Guide for Learning How to Mill Your Own Flour. It walks you through everything you need to feel confident using fresh milled flour in your kitchen. 

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If you make this recipe, please leave a rating on the recipe card below! I’d also love for you to tag me @autumn.chasingoursimple on Instagram so I can see what you’ve been baking!