These bakery style sourdough discard double chocolate muffins are a decadent treat. Made with chocolate chips and cocoa powder, these muffins are a delight to eat. They are perfect to enjoy with a loved one during Valentine’s Day!

If you give a moose a muffin, make sure it is sourdough! We are all about a good bakery style sourdough muffins in this house and for a good reason.

These sourdough discard double chocolate muffins are exactly what we were dreaming of when craving chocolate. Made with sourdough discard, sour cream, butter, milk and eggs for moisture – we think these might be the best sourdough chocolate muffins we have made to date.

It is always a compliment when my husband (the ultimate taste tester), tells me these have a rich chocolate flavor and are worthy of being on the blog. When he came back for second just moments after finishing a muffin (on a full stomach, I might add), I knew these ones fit the bill.

Similar to our sourdough double chocolate donuts, this recipe includes both cocoa powder and chocolate chips for flavor. The chocolate chips are also on top with Turbinado sugar.

Just be sure if you are giving these to kiddos – you are aware of the power of chocolate before nap time. While delicious, they certainly give the best chocolate ‘buzz’!

hand grabbing double chocolate chip muffin

Why you will love these

The recipe can be adapted to stir and go or long fermented. Those with a gluten sensitivity (myself included), have options.
These can be made with sourdough discard or active sourdough starter; they are a great way to use up sourdough discard

Each muffin looks straight out of a bakery as they are tall in height and sprinkled with chunks of sugar (aka bakery-style muffins!)
They are light, fluffy and full of flavor

They have multiple types of chocolate to solve the chocolate craving
The recipe has adaptable ingredients

Kitchen Equipment

There are a few pieces of kitchen equipment which make this recipe easy. This recipe comes tougher er easily with a hand mixer or whisk – not a stand mixer.

Ingredients for Sourdough Discard Double Chocolate Muffins

This recipe is easily adapted to fit the ingredients you have on hand and any food intolerances or allergies. These muffins, similar to our sourdough banana muffins, are made with simple ingredients.

Flour
- All purpose flour, spelt flour or gluten free flour work well within this recipe. A 1-to-1 Gluten free flour is easy to use within this recipe when made as a ‘stir and go’ option. You could also use whole wheat flour in small quantities – though it will change the texture of the fina.
White Sugar
- Without sugar this recipe would be bitter. Do not fear, the recipe is not ‘too sweet’ and will cure your sweet tooth.
Cocoa powder
- Unsweetened cocoa powder or Hersheys special dark cocoa work well within this recipe. Special dark cocoa is treated with alkaline which increases the intensity of the cocoa flavor.
Baking soda
- Optional based on recipe choice – stir and go vs long fermented
Baking powder
- Optional based on recipe choice – stir and go vs long fermented
Salt
Vanilla extract
- A sweet recipe is always better with vanilla extract
Sour cream
- Sour cream provides an additional layer of moisture within the muffin. Because of the moisture content, you can use plain yogurt or plain greek yogurt as an alternative.
Milk
- To provide rich flavor known within bakery style muffins, use milk instead of water.
Butter
- Unsalted butter provides a rich flavor within these muffins
- Coconut oil, avocado oil or vegetable oil can be used within this recipe, though the muffins are not as moist as when butter is used.
Sourdough discard
- This recipe can be adapted to stir and go or long fermented. For stir and go, either active starter or sourdough discard will work as additional leavening agents – baking soda and baking powder, are required. For long fermented, active sourdough discard works best as it will provide rise to the muffins over an extended period of time.
Eggs
- In addition to the leavening agent, the eggs provide rise within the muffins.
Chocolate chips
- Any type of chocolate chips will work within this recipe. Mini chocolate chips, milk chocolate chips, dark chocolate chunks chips, and semi-sweet chocolate chips are our favorite.
Turbinado sugar
- These large crystals of sugar provide extra shimmer to the muffin tops, and a slight crunch on top with each bite.

sourdough double chocolate muffins on cooling rack

How to make Sourdough Discard Double Chocolate Muffins

There are two options to make these double chocolate sourdough muffins- stir and go or long fermented.

Stir and go timeline

To make sourdough double chocolate chip muffins, start by preheating the oven to 425 degrees Fahrenheit. Using a whisk or a kitchenaid hand mixer, combine the wet ingredients in a mixing bowl.

Add the wet ingredients to the center of the dry ingredients and still until combined.

To a greased muffin tin, alternate filling the muffins into every other section to ensure six are filled. Fill each portion 3/4 of the way full to achieve a tall, bakery style muffin.

To make equal muffins – use a large cookie scoop. Sprinkle with turbinado sugar and chocolate chips.

Bake in the oven for 5 minutes before reducing the temperature to 350 degrees. Cook for 12-15 minutes, or until the tops are firm to the touch and the centers come out clean when poked with a toothpick.

bakery style sourdough double chocolate muffins

Place on a cooling rack to cool completely before storing.

Long fermented timeline

To make long fermented sourdough discard double chocolate muffins, combine water, sourdough starter, melted butter, cocoa powder, salt, sugar and flour together in a large bowl. Stir together until combined.

The mixture will be thick in texture, similar to a cookie dough, not thin like a muffin batter. This is due to allowing certain ingredients to ferment on the countertop prior to completing the recipe.

Cover the bowl with a lid. Allow to ferment on the countertop for 12-14 hours, or long enough to meet your fermentation goals.

Add the remaining ingredients (vanilla extract, sour cream, eggs and chocolate chips) prior to placing in the fridge if bulk fermenting longer. Otherwise, bake straight away, stirring in the baking soda and baking powder.

Pour batter into a muffin tin, being sure to fill each spot 3/4 of the way full and alternating spots filled (6 in total). Top with remaining chocolate chips and sugar before placing in the oven to bake.

Store in the fridge for up to 3 days before baking. When ready to bake, remove from the fridge and allow to warm up to room temperature.

Stir in the baking soda and baking powder right before baking for the best oven spring. Top with sugar and chocolate chips, following the baking instructions outlined above.

How to store Sourdough Double Chocolate Muffins

To store these muffins at room temperature, place them in a ziplock bag for up to 3 days. Due to the sour cream, refrain from keeping them on the countertop much longer.

Store them in the fridge in a bag or airtight container for up to a week. Wrap in plastic wrap to ensure they last in the freezer for an extended period of time – up to 3 months. To reheat, remove from the fridge or freezer and place in the microwave with a pat of butter.

Frequently Asked Questions

To make bakery style muffins:

Ensure the muffin tin is filled at least 3/4 of the way full
Use diary products for rich and decadent muffins
Top the muffins with the flavorings inside the muffins and sprinkle with Turbinado sugar
Bake the muffins in a tin with only 6 at a time.
- By giving the muffins more space, they will cook evenly and have more oven spring.
Start with oven temperature at 425 for 5 minutes and reduce to 350 for the remainder of the cooking time to increase oven spring.

If you can not find turbinado sugar, crushed sugar cubes work the same. Alternatively, sugar in the raw after often larger sized crystals as well.

Plain white sugar will not work due to the granulated texture and size. Coconut sugar can be utilized, though it is not as chunky as turbinado sugar.

Yes, walnuts and pecans are the best types of nuts. Add up to 1/2 cup.

Yes – you can add an espresso shot to these muffins. Add one espresso shot and reduce the overall liquid by 2 TBS. You can also use strongly brewed coffee.