Sourdough Discard Apple Muffins are perfect for the fall and winter when apples are in season! They're warm, a little nutty (from the nutmeg and cinnamon, but you can also add chopped nuts if you like!), and so comforting. They're also a great way to use up some sourdough discard, and the batter doesn't need any rise time (unlike other bread recipes).

If you're looking for other apple recipes, try this Sourdough Discard Apple Pull Apart Bread. And if you're looking for other sourdough discard recipes, check out these Sourdough Discard Pancakes, Sourdough Discard Waffles, and Sourdough Discard Cinnamon Rolls.
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Why you'll love this recipe
- This easy Sourdough Discard Apple Muffins recipe comes together in about 15 minutes. You'll have warm muffins on the table in under an hour!
- This recipe is easy to adapt to make with different types of apples, pears, or a combination of the two! You're aiming for about 1 ¼ cups of diced apples or pears.
- Muffins are a great way to use some of your sourdough discard, and the dough (or batter, in this case) doesn't need any rise time.
- The cinnamon and nutmeg give these muffins a great nutty fall flavor that is so warm and comforting.
Ingredients
There are only a few key ingredients you'll need to pull these muffins together.

- Unsalted butter: It's important this is softened (at room temperature) so it creams together correctly with the granulated sugar.
- Granulated sugar: This isn't a low-sugar recipe, but I promise it's worth it!
- Eggs: The eggs should be at room temperature for this recipe.
- Sourdough discard: The sourdough discard should be unfed and at room temperature for this recipe. This recipe is designed for a sourdough starter using a 1:1:1 ratio (when you feed your starter it's with 1 part starter, 1 part flour, 1 part water). If your starter uses a different ratio, you may need to adjust some of the ingredients in this recipe.
- Apple: I like to use Gala apples, but other types that work well are Jonagold, Honeycrisp, Braeburn, Fuji, Granny Smith and Pink Lady apples. A small dice will be best!
- Turbinado sugar: I recommend sprinkling the muffins with 1 Tablespoon of turbinado sugar before baking. This adds a bit of crunchy sweetness to the top, without having to make a separate topping or crumble. I like to use Sugar in the Raw.
See full recipe below for detailed directions.
Substitutions & Variations
This is a very adaptable recipe and below are a few easy substitutions and variations you can try.
- Use pears - Use a combination of apples and pears, or only pears to make pear muffins!
- Use an egg substitute - If you're not baking with eggs, you can use a liquid egg substitute (such as Just Egg) for this recipe.
- Use active sourdough starter - If you'd rather use active sourdough starter instead of discard, you can! To do so, omit the baking powder and replace the sourdough discard with active starter (in a 1:1 substitute).
- Add nuts - Fold ½ cup chopped nuts (such as walnuts, pecans or almonds) into the batter with the diced apples. Continue baking as directed.
- Add dried cranberries - Fold ½ of dried cranberries into the batter with the diced apples. Continue baking as directed.
I have not tested this recipe with other variations, but if you do, let us know how it turns out in the comments! I always love to hear how you're adapting these recipes and use those as ideas for future recipes as well!
How to make Sourdough Discard Apple Muffins
These muffins come together in a few easy steps!

In a large bowl, cream the softened butter and granulated sugar until light and fluffy, about 2-3 minutes.

Add the eggs, one at a time, beating in between. Mix in the vanilla extract.

In a small bowl, combine the flour, baking powder, cinnamon, nutmeg and salt.

Mix in the sourdough discard, then add the dry ingredients and mix until no dry spots remain.

Chop your apples into a small dice.

Add the diced apples to the batter and fold until evenly distributed.

Divide the batter among the muffin cups (a cookie scoop is great to use here!). Sprinkle with turbinado sugar and bake until golden brown.

Once baked, let cool in the pan for 10 minutes and then serve or transfer to a cooling rack to cool fully.
Expert Baking Tips
- Make sure to cream the butter and sugar long enough. This is the foundation of this recipe, so spend the 2-3 minutes to get a really nice, smooth and creamy butter and sugar mixture!
- This won't work if your butter is not softened at room temperature. Butter that is too hard or too soft (melted) will not cream correctly.
- Line your muffin pan with muffin liners. You can either use storebought muffin cups (or these silicone cups), or make your own parchment paper liners.
- Chop the apples to a small dice. This way, it's easier to distribute the apples in the dough so you'll end up with apples in every bite of muffin! Also, no need to peel the apples.
- Don't forget the turbinado sugar! This adds a nice crunchy sweet layer to the top of the muffins.

What is sourdough discard?
Sourdough discard is what is leftover after you feed your sourdough starter. You can either literally discard it (throw it away or compost it), or use it in sourdough discard recipes like this one.
Every sourdough starter, and therefore discard, is different. If your batter seems too wet or too dry, add more flour or non-dairy milk (1 Tablespoon at a time) to reach your desired consistency.
If you are new to working with sourdough starter, check out these in-depth posts on how to feed sourdough starter and how to use sourdough discard.
Equipment
These muffins can be made with a few large mixing bowls and a wooden spoon (I love a GIR Spoonula for mixing!). You will need a hand-held mixer to cream the butter and sugar.
You'll need a 12-cup muffin pan and muffin liners (you can use regular muffin liners, parchment paper muffin liners, or silicone muffin liners). I also recommend using a cookie scoop to scoop the batter into the muffin cups.
Storage
Room Temperature Storage: Store Sourdough Discard Apple Muffins in an airtight container at room temperature for up to 3 days. You can reheat them in the microwave for 15-30 seconds to make them warm and soft again.
Freezer Storage: These muffins freeze very well. Let them cool completely, then transfer to an airtight container or bag and freeze for up to 3 months. You can also leave the muffin liners on for freezing! To reheat, let the muffins thaw at room temperature, or reheat in the microwave for 30-60 seconds.

Recipe FAQ
Yes, you can! To do so, omit the baking powder and replace the sourdough discard with active sourdough starter (in a 1:1 substitute).
I highly recommend sprinkling the top of the muffins with turbinado sugar. This gives a nice crunchy, sweet topping. I like to use Sugar in the Raw. But it is optional and you can omit this if you prefer!
Yes! This would work particularly well with other types of apples or pears. There are other variation suggestions in the "substitutions and variations" section above.
I highly recommend using muffin liners to make it easier to remove the muffins from the pan. If you'd rather not use them, make sure to grease your pan well before adding the batter.
No! You can leave the peel on. A small dice for the apples works best so they distribute evenly throughout the batter (and you'll end up with apples in every bite of the baked muffins!).

Sourdough Discard Apple Muffins
Ingredients
- ½ cup unsalted butter softened
- 1 cup granulated sugar
- 2 eggs room temperature
- 1 teaspoon vanilla extract
- 200 grams (about ¾ cup) sourdough discard unfed, at room temperature
- 1 cup all-purpose flour
- 1 ½ teaspoons baking powder
- 1 ½ teaspoons ground cinnamon
- ½ teaspoon kosher salt
- ½ teaspoon ground nutmeg
- 1 apple diced (about 1 ¼ cups)
- 1 Tablespoon turbinado sugar
Instructions
- Preheat the oven to 375°F and line a 12-cup muffin pan with muffin liners. Set aside.
- In a large bowl, use a hand-held blender to cream together the softened butter and granulated sugar until light and fluffy, about 2-3 minutes. Add eggs, one at a time, mixing in between each. Stir in vanilla extract.
- Stir in sourdough discard. Depending on your sourdough discard, you may need to add a little non-dairy milk or more flour (1 Tablespoon at a time) to reach your desired batter consistency.
- In a small bowl, whisk together the flour, baking powder, cinnamon, salt and nutmeg. Fold into the batter mixture and stir just until no dry spots remain.
- Fold the diced apples into the batter, stirring until evenly distributed.
- Spoon the batter into the prepared muffin liners, filling each cup (a cookie scoop works well for this!). Sprinkle with turbinado sugar and bake for 30-35 minutes until golden brown. Let the muffins cool in the pan for 10 minutes, then transfer to a cooling rack to cool fully.
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