The Best Sourdough Chocolate Chip Muffins Recipe

I make muffins every week to have on hand for breakfast and snacks. Recently, we were snowed in and I decided to convert the recipe to a long fermented one. These sourdough chocolate chip muffins are the best muffins I’ve ever made!

Muffins are one of the easiest recipes to make if you are new to bread baking or using freshly milled flour.

This post contains affiliate links. I may make a small commission on sales at no extra cost to you

This recipe is a great way to use up leftover sourdough discard.

Why I love this recipe

Made with simple ingredients and free of refined sugar, these are delicious muffins that are easy to make and perfect for breakfast or as a great snack.

The sourdough starter adds a subtle tang to the perfectly sweet muffins.

Check out all of my Sourdough Recipes

Why Sourdough?

Sourdough is a process of fermenting your bread dough with a sourdough starter.

This process breaks down the gluten and proteins that can sometimes be hard to digest for gluten sensitive people.

In order to get the most benefits of the fermentation process, you need to let your dough ferment for at least 12-24 hours.

As you can see, the process of sourdough can be very helpful for many people. If you’ve never made a Sourdough Starter it’s easy and fairly quick to do.

The great news is that once you have an active starter, as long as you maintain it, it will last for as long as you want it.

There are starters that have been handed down through generations!

What is Active Sourdough Starter?

Active starter is starter that has been fed within the last 24 hours and is bubbly and active.

What is Sourdough Discard?

Sourdough starter discard is starter that is hungry. It hasn’t been fed recently and may have a liquid on top and an acetone odor.

I use freshly milled flour for all of my baked goods and nowhere does that flour shine more than muffins, in my opinion.

For this recipe I use hard red wheat, but you can use any flour you have on hand.

To mill my wheat berries, I use the Nutrimill Classic Grain Mill

What you will need to make chocolate chip sourdough muffins

1. Flour– I use freshly milled flour. You can use all purpose flour, bread flour, or whole wheat flour.
2. Sourdough Starter– You can use active sourdough starter or sourdough discard.
3. Milk– (I use milk kefir) you can use buttermilk, whole milk, or a dairy alternative
4. Olive oil– You can substitute with vegetable oil, melted butter, or melted coconut oil.
5. Honey
6. Egg
7. Salt
8. Baking powder
9. Baking soda
10. Chocolate chips– (I like the mini chocolate chips) You can use semi-sweet chocolate chips or white chocolate chips.
11. Vanilla extract

For full ingredient amounts, see recipe card below

How to make Sourdough Chocolate Chip Muffins

The night before you want to make these, in a large bowl combine the wet ingredients of the starter and milk. Mix until cloudy. Add the flour.

Stir well, cover with plastic wrap and let sit at room temperature overnight or up to 24 hours for long fermentation.

The next day, add the other ingredients.

You will need to stir for a few minutes to combine all the ingredients. But, it will come together. A stand mixer with a cookie paddle can be used to make it easier.

Preheat the oven to 400 degrees F.

Scoop muffin batter in 12 cup muffin tin lined with muffin liners, paper liners or sprayed with oil.

Bake for 15 minutes or until a toothpick comes out clean.

Cool on a cooling rack or wire rack before storing.

Try my Sourdough Chocolate Chip Cookies recipe.

For another sourdough muffin recipe, try my Sourdough Blueberry Muffins

Storage Tips

Store in an airtight container on the counter for 3-4 days.

Freeze in freezer safe bags for up to 3 months.