Sourdough Double Chocolate Chip Muffins
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If you’re a chocolate lover, these sourdough double chocolate chip muffins are the perfect sweet treat that can be whipped together in about 30 minutes. Use up your sourdough discard or active sourdough starter to make these soft, fluffy muffins!

These are truly the moistest, fluffiest chocolate sourdough muffins ever. The plain, full-fat Greek yogurt makes them incredibly soft–but there are more parts at play than just the ingredients.
Ensuring you use room-temperature ingredients plays a huge part–along with avoiding over-mixing once you’ve incorporated the wet and dry ingredients.
They make a great snack for the kids (and yourself) and are a lovely way to use up extra sourdough discard (or active starter!).
Looking for more sourdough recipes? Check these out:
- sourdough banana chocolate chip muffins
- sourdough vanilla bean muffins
- sourdough apple carrot muffins
Ingredients
- All-purpose flour – bread flour also works!
- Cocoa powder (or Dutch-processed cocoa powder) – I used Dutch-processed cocoa powder because I love the depth of flavor it adds, but both work great.
- Baking powder
- Baking soda
- Salt
- Extra virgin olive oil – high-quality, light-flavored extra-virgin olive oil or other neutral oil works for this recipe
- Granulated sugar
- Eggs – room temperature eggs work best here!
- Greek yogurt – make sure it is plain, full-fat yogurt (this is what makes these muffins so soft and fluffy). Alternatively, you can use sour cream. Make sure these ingredients are room temperature.
- Whole milk – room temperature whole milk works best, though any kind of milk will work!
- Sourdough discard – room temperature sourdough discard or active, bubbly sourdough starter
- Vanilla extract
- Semi-sweet chocolate chips – for mixing into the batter and topping the muffins with before baking. You could also use dark or milk chocolate.

Step-By-Step Instructions

Step 1: Preheat the oven
Preheat your oven to 350°F (175°C). Line a 12-cup muffin pan with paper liners or lightly grease each cup (see tips for making bakery-style muffins below if you’d like to make the BEST muffins).
Step 2: Sift the dry ingredients
In a large mixing bowl, sift together the all-purpose flour, cocoa powder, baking powder, baking soda, and salt. Sifting removes lumps from the cocoa powder and helps evenly distribute the leavening agents.
Step 3: Mix the oil and sugar
In a separate bowl, whisk together the olive oil and granulated sugar until the mixture is smooth and well combined.
Step 4: Add the eggs
Add the eggs to the sugar mixture and whisk until the mixture becomes slightly thick and glossy.
Step 5: Add the remaining wet ingredients
Whisk in the Greek yogurt, whole milk, sourdough discard, and vanilla extract until the mixture is smooth and fully combined.

Step 6: Combine wet and dry ingredients
Slowly pour the wet ingredients into the bowl with the dry ingredients. Gently mix with a spatula or wooden spoon until the batter is just combined. Be careful not to overmix.
Step 7: Fold in the chocolate chips
Gently fold in the semi-sweet chocolate chips, distributing them evenly throughout the batter.

Step 8: Fill the muffin pan
Divide the batter evenly among the muffin cups. If desired, sprinkle a few extra chocolate chips on top of each muffin.
Step 9: Bake
Bake for 20–25 minutes, or until a toothpick inserted into the center comes out with a few moist crumbs.
Step 10: Cool the muffins
Allow the muffins to cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely before serving.

Tips for the Best Bakery-Style Muffins
- Use room-temperature ingredients.
- Avoid over-mixing! This can make them dense.
- Allow your muffin batter to rest for 20-30 minutes if time allows. Giving it this extra time will help with the rise of the muffins while they bake.
- Line every other muffin cup and fill with batter up to the top. Lining every other muffin cup allows the muffins to rise and not be crowded.
- Top each with several chocolate chips right before baking.
Equipment Needed
- 12-cup muffin pan
- Paper muffin liners (optional)
- Large mixing bowl
- Medium mixing bowl
- Sifter or fine-mesh sieve
- Whisk
- Spatula or wooden spoon
- Measuring cups and spoons
- Cooling rack
- Toothpick (for testing doneness)

Storage
Room Temperature: Store cooled muffins in an airtight container at room temperature for up to 3 days.
Refrigerator: Keep muffins in an airtight container in the fridge for up to 1 week. Allow to come to room temperature or warm slightly before serving.
Freezer: Place cooled muffins in a freezer-safe bag or container. Freeze for up to 3 months. Thaw at room temperature or warm gently in the microwave or oven before serving.

Sourdough Double Chocolate Chip Muffins
Ingredients
Dry Ingredients
- 1 ½ cups all-purpose flour
- ½ cup cocoa powder natural or Dutch-processed, unsweetened
- 2 teaspoons baking powder
- 1 teaspoon baking soda
- ¼ teaspoon salt
Wet Ingredients
- ½ cup extra virgin olive oil
- 1 cup granulated sugar
- 2 large eggs room temperature
- ½ cup Greek yogurt plain, full-fat, room temperature
- 1 cup whole milk room temperature
- ½ cup sourdough discard room temperature
- 1 teaspoon vanilla extract
Mix-Ins
- 1 ½-2 cups semi-sweet chocolate chips
Instructions
Prepare the Oven and Pan
- Preheat your oven to 350°F (175°C). Line a standard 12-cup muffin pan with paper liners or lightly grease each well. **read recipe note tips below for bakery-style muffins
Combine the Dry Ingredients
- In a large mixing bowl, sift together the flour, cocoa powder, baking powder, baking soda, and salt. Sifting helps remove cocoa lumps and ensures the dry ingredients are evenly distributed.
Mix the Wet Ingredients
- In a separate bowl, whisk together the olive oil and granulated sugar until smooth and well combined.
Combine the Batter
- Slowly pour the wet ingredients into the bowl of dry ingredients. Using a spatula or wooden spoon, gently mix until just combined. Be careful not to overmix, as this can make the muffins dense.
- Fold in 1½–2 cups of chocolate chips, distributing them evenly throughout the batter.
Fill the Muffin Pan
- Divide the batter evenly among the prepared muffin cups. Top each with a few extra chocolate chips.
Bake
- Bake in the preheated oven for 20–25 minutes, or until a toothpick inserted into the center comes out with just a few moist crumbs (melted chocolate is fine).
Cool
- Allow the muffins to cool in the pan for 5 minutes, then transfer them to a wire rack to cool completely.
Notes
- Use room-temperature ingredients.
- Avoid over-mixing! This can cause them to be dense.
- Allow your muffin batter to rest for 20-30 minutes if time allows. Giving it this extra time will help with the rise of the muffins while they bake.
- Line every other muffin cup and fill with batter up to the top. Lining every other muffin cup allows the muffins to rise and not be crowded.
- Top each with several chocolate chips right before baking.
- Room Temperature: Store cooled muffins in an airtight container at room temperature for up to 3 days.
- Refrigerator: Keep muffins in an airtight container in the fridge for up to 1 week. Allow to come to room temperature or warm slightly before serving.
- Freezer: Place cooled muffins in a freezer-safe bag or container. Freeze for up to 3 months. Thaw at room temperature or warm gently in the microwave or oven before serving.

These are truly so soft and fluffy! My kiddos devoured these. If you make them and enjoy them, it would mean the world to me to hear your thoughts!