Chocolate-Chocolate Chip Sourdough Muffins

I love my sourdough starter. I find many ways to use it in recipes in the kitchen. This is one of the recipes that I love to make because I simply love chocolate. A sourdough starter is easy to maintain and keep. You can check out my sourdough starter recipe on my blog here if you want to start your own starter. It is two simple ingredients and a lot of time and love. You can use sourdough starter in various recipes that call for yeast. That said, it is not just a mix; let rise for an hour or two in a warm place and then bake it. Sourdough does not work like that. It needs time and a few “stretch and folds” to make beautiful loaves of bread.

This recipe for my chocolate-chocolate chip sourdough muffins uses the discard of the sourdough starter. A sourdough discard is a discard that you usually toss or use in recipes before refeeding your starter for loaves of bread. There is nothing wrong with a discard and it is very tasty in desserts, pancakes, pizza crusts, or used as a topping for one-pan meals that calls for a crust on top. I am always finding ways to make something out of my discard instead of just throwing it away. I hate wasting good sourdough.

I love using sourdough because I have a sensitivity to a yeasted dough. I can eat them. They just don’t like me very well sometimes so I usually opt for making either my own yeasted bread/desserts or sourdough bread/desserts. They are so much better and they tend to not upset my stomach and that is a good thing.

Let me share with you how I make these tasty little muffins.


1/2 cup of Sourdough Starter or Discard
2 Eggs – room temp
1/4 cup. Neutral Oil – I use avocado or coconut oil
1 tsp. Vanilla Extract
1 1/3 cup. Milk
1/2 cup. Cocoa Powder
1/2 to 3/4 cup. Sugar ( This depends on how sweet you want your muffins)
2 1/2 cups. All-Purpose Flour
3 tsp. Baking Powder
1/4 tsp. Baking Soda
1/2 tsp. Kosher Salt OR 1/4 tsp. Fine Salt
1 cup. Chocolate Chips (plus more for the top of the muffins later)


  1. Preheat the oven to 350*. Grease or line a muffin tin with either butter, oil, or muffin liners. You can also use silicone muffin pans. Set aside.
  2. In a large bowl add the sourdough starter, eggs, oil, vanilla extract, milk, and sugar. Whisk together until well combined.
  3. Add the cocoa powder, flour, baking powder, baking soda, and salt. Whisk until just combined and smooth.
  4. Switching to a wooden spoon or rubber mixing spoon, Add in the chocolate chips and fold them in until just combined. Let this mixture stand for about 30 minutes just to activate the sourdough Or you can leave out the eggs and let it ferment overnight and then add the eggs in and mix. Whichever you prefer will do just fine.
  5. Using a 1/3 cup measuring cup or ice cream scoop, scoop the batter and place it in the prepared muffin pan. Leave a little room at the top so they can expand and bake in the oven. If you overfill the muffin pan with batter then it will become very messy when baking. It will drip over the sides and become flat on the top and not round like a muffin should be.
  6. Once the batter is in the muffin pan, you can sprinkle extra chocolate chips on the top. This just makes the tops look good and plus you have extra chocolate chips and that is never a bad thing. Just make sure you have an equal amount of batter in the pan so they all cook evenly and there are no muffins left undercooked in the center.
  7. Bake in a preheated oven at 250* for 18 to 22 minutes or until a toothpick comes out clean when stuck into the center of the muffins.
  8. Remove from the oven and let cool for about 30 to 40 minutes in the pan and then remove them from the silicone mold to cool completely. If you are using a metal muffin tin then let them cool almost completely then transfer them to a wire rack to cool the rest of the way. If you are using liners then you can let them cool for about 10 minutes and then transfer them to a wire rack to cool completely.
  9. Store in an airtight container on the counter for 2 to 3 days max then transfer them to the fridge in an airtight container or zip lock bag. OR you can store them directly in the fridge for up to 1 to 2 weeks. They freeze well so just make sure to thaw them completely before consuming them. You can also heat these up in the oven for about 5 minutes to warm them through or in the microwave for about 15 to 20 seconds. They go great with ice cream when warmed through.

  • If you do not want to use cocoa powder and just make a simple muffin with chocolate chips, then simply omit the cocoa powder and add the same amount of flour that you would have used for the cocoa powder. Then follow the directions as they will bake up the same.
  • You can omit the cocoa powder and chocolate chips and add in blueberries, diced strawberries, raspberries, blackberries, mixed berries, or any sort of nuts like pecans, walnuts, sunflower seeds, pistachios, or a variety of any fruit or nut that you like. The sky is the limit.
  • You can omit the cocoa powder, chocolate chips, and neutral oil and add in orange juice, orange zest, and olive oil to make an Italian-style olive oil muffin.
  • Omit the cocoa powder and chocolate chips and add in lemon zest, lemon juice, and poppy seeds for a lemon poppy seed muffin. These are so good.
  • To the original batter, you can mix up 1/2 a block of cream cheese (room temp), 1 egg, and 1/4 cup of powdered sugar until smooth. Fill the muffin tin halfway with the batter. Add in about 1 tsp of the cream cheese mixture and then add more chocolate batter on top of that. Top with more chocolate chips and bake until a toothpick comes out with a few moist crumbs.
  • This base batter can be used and you can swap out the ingredients for whatever flavor you prefer.

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