How to Make Chocolate Sourdough Muffins That Taste Better Than Store-Bought

A Soft, Moist, Chocolate Dream Right From Your Kitchen

There’s something deeply comforting about the smell of fresh chocolate muffins baking in the oven. Now imagine that comfort, mixed with the satisfaction of using your own sourdough starter to create a dessert that’s richer, softer, and far more flavorful than anything you’d find on a store shelf.

These chocolate sourdough muffins are a game-changer—especially if you’ve been baking sourdough bread and wondering what to do with the leftover starter. Instead of tossing it, you can turn it into a batch of warm, gooey chocolate muffins that your whole family will ask for again and again.

They’re simple to make, freezer-friendly, and incredibly moist thanks to the sour cream and oil combo. Whether you’re baking for a family gathering, a cozy weekend treat, or just something sweet to go with your coffee, these muffins never disappoint.

this RECIPE

Ingredients

Before you get started, gather your ingredients. Each one plays a role in building that perfect texture and deep chocolate flavor.

• 2 cups (240 g) all-purpose flour
• ½ cup (45 g) cocoa powder (regular or dark)
• 2 teaspoons baking powder
• ½ teaspoon baking soda
• 1 teaspoon (5 g) salt
• ½ cup (125 g) unfed sourdough starter
• ½ cup (120 g) avocado oil or vegetable oil
• 1 cup (200 g) granulated sugar
• 2 large eggs
• ¾ cup (185 g) sour cream
• 2 teaspoons (10 g) vanilla extract
• ¼ cup (60 g) milk
• 1 ¾ cups (315 g) semi-sweet chocolate chips

Instructions

Step 1: Preheat and Prep

Preheat your oven to 425°F (218°C). Position the rack in the center of the oven for even heat circulation. Line a muffin tin with paper liners or use parchment muffin cups for a bakery-style look.

Step 2: Mix Dry Ingredients

In a large bowl, whisk together the flour, cocoa powder, baking powder, baking soda, and salt. This step ensures all the dry ingredients are well combined and lump-free, helping the batter mix evenly later.

Step 3: Whisk Wet Ingredients

In a separate bowl, combine the oil, sugar, eggs, sour cream, milk, vanilla extract, and sourdough starter. Use a whisk to mix until smooth. The mixture should be creamy and slightly thick.

Step 4: Combine Wet and Dry

Pour the wet mixture into the bowl with the dry ingredients. Gently fold them together using a spatula or wooden spoon. Be careful not to overmix—stop as soon as no dry flour is visible. This helps keep your muffins tender.

Step 5: Add Chocolate Chips

Fold in the chocolate chips evenly so every bite gets a little chocolate love. If you’d like, save a few to sprinkle on top of the muffins before baking.

Step 6: Fill the Muffin Tins

Using an ice cream scoop or large spoon, fill each muffin liner to the top. This gives you those beautiful high bakery-style muffin tops.

Step 7: Bake

Bake the muffins at 425°F (218°C) for 5 minutes. Then, without opening the oven, lower the heat to 350°F (176°C) and continue baking for 15–18 minutes. The initial high temperature helps the muffins rise quickly.

Step 8: Cool

Once baked, remove the tray from the oven and allow the muffins to cool completely in the tin before removing. This keeps them from falling apart while still warm.

Baking Tips

Don’t skip the two-temperature baking method. Starting at 425°F helps create a tall, rounded muffin top.

Avoid overmixing. It can cause dense muffins. Stir just until combined.

Add toppings. Sprinkle extra chocolate chips, chopped nuts, or coarse sugar on top before baking for texture and flavor.

Use parchment liners. They not only look beautiful but prevent sticking without any greasing.

Room temp ingredients work best. This helps them combine more easily and bake evenly.

Storage & Freezing

Short-Term Storage

Store the muffins in an airtight container at room temperature for up to 3 days. If your home is warm, store them in the fridge to keep them fresh.

Freezing Instructions

Once the muffins are completely cooled, wrap each one in plastic wrap and store them in a freezer-safe zip-top bag. They’ll keep well for up to 2 months. To enjoy, thaw at room temperature or warm in the microwave for 20–30 seconds.

Serving Suggestions

These chocolate sourdough muffins are incredibly versatile and can be enjoyed in so many ways depending on the occasion.

Morning Treat
Pair a warm muffin with your morning coffee or tea for a cozy start to the day. The richness of the chocolate goes especially well with a bold roast or a smooth black tea.

Afternoon Pick-Me-Up
Need a break during the day? Enjoy one with a glass of cold milk or a hot latte. They make a perfect snack when you need something sweet but satisfying.

Brunch Addition
Serve these muffins as part of a weekend brunch spread alongside fresh fruit, yogurt, and eggs. They add just the right touch of indulgence without overpowering the meal.

Dessert Idea
Warm a muffin slightly and top it with a scoop of vanilla ice cream for an easy, impressive dessert. You can even drizzle a little melted chocolate or caramel sauce on top.

On the Go
These muffins travel well, making them perfect for packed lunches, road trips, or a quick bite before running errands. Wrap them individually for a grab-and-go option.

Sourdough Starter Info

What is Unfed Sourdough Starter?

Unfed starter, also known as “discard,” is the portion you remove before feeding your sourdough. While it’s not active enough to make bread rise, it’s perfect for baking recipes like muffins, pancakes, and cakes.

Why Use It?

It gives baked goods a beautiful depth of flavor and helps avoid food waste. In these muffins, it adds moisture and a slight tang that balances the sweetness of the chocolate.

Chocolate Chip Variations

Want to make the recipe your own? Try these fun twists:

White chocolate chips – Add a creamy sweetness.
Dark chocolate chunks – For intense chocolate lovers.
Mint chips – A refreshing twist for the holidays.
Peanut butter chips – A classic chocolate-peanut combo.
Chopped walnuts or pecans – Add a crunch and nutty flavor.

Feel free to mix and match—just keep the total mix-ins to around 1¾ to 2 cups.

Frequently Asked Questions (FAQ)

Can I use active sourdough starter instead of discard?

Yes, you can use active starter. The flavor will be slightly milder, but the recipe will work the same.

Can I make these muffins gluten-free?

Yes, you can substitute the flour with a gluten-free 1:1 baking blend. Just make sure it includes xanthan gum.

Can I use yogurt instead of sour cream?

Full-fat Greek yogurt works great as a substitute for sour cream and provides a similar texture.

Why start baking at a higher temperature?

Starting at 425°F helps the tops rise quickly, giving you those tall, bakery-style muffin tops. Lowering the temperature afterward prevents them from drying out.

Can I make mini muffins?

Absolutely. Just reduce the baking time to about 10–12 minutes at 350°F after the initial 5-minute high-temp burst.

Conclusion

These chocolate sourdough muffins are more than just a clever way to use up leftover starter—they’re a rich, delicious treat that’s sure to become a household favorite. Moist, chocolatey, and simple to make, they offer bakery-quality flavor right from your own kitchen.

If you’ve been looking for a new way to love your sourdough, this is it. Give them a try, and watch them disappear from the plate faster than you can say “chocolate.”

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