As apple picking season is in full swing, there's nothing quite like the warm, cinnamon-kissed aroma of homemade muffins filling your kitchen. This delicious recipe for sourdough discard apple cinnamon muffins brings together tart, orchard-fresh apples, warm spices, and the subtle tang of sourdough starter, turning leftover discard into a fall treat that tastes like a sourdough apple pie in muffin form. Each bite is bursting with autumn flavor, from tender apple pieces to cinnamon and a hint of nutmeg.

Making these muffins is an irresistible way to celebrate the season. Whether you're looking to use up sourdough discard or just craving a comforting baked good on a crisp fall day, these muffins invite you to savor the cozy flavors of fall.

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Fall is one of our favorite times of year around here, the crisp air, the changing leaves, and all the cozy flavors that come with it. These apple cinnamon sourdough muffins are a staple in our kitchen once the weather starts to turn. We enjoy them so much! They’re soft, warmly spiced, and just sweet enough. And the smell! When they’re baking, the whole house fills with the most comforting aroma of apples and cinnamon. It instantly sets the tone for the season and makes everything feel a little more peaceful, a little more homey.

Ingredients for the Apple Cinnamon Sourdough Muffins
Dry Ingredients
- 2 cups (240g) all-purpose flour (or fresh milled wheat)
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 ½ teaspoons cinnamon
- ½ teaspoon nutmeg
Wet Ingredients
- 1 cup (100g) sourdough starter discard or active sourdough starter
- ¾ (150g) cup light or dark brown sugar to be mixed with wet ingredients
- ½ cup melted unsalted butter
- 2 large eggs
- 1 ¼ cups milk
- 1 teaspoon vanilla extract
Add-Ins
- 1 ¼ cups finely chopped crisp apples (peeled or unpeeled)
Crumble Topping:
- ½ cup all-purpose flour
- ½ cup brown sugar (packed)
- ½ teaspoon ground cinnamon
- ¼ teaspoon salt
- ¼ cup cold unsalted butter (cubed)
Sourdough Apple Cinnamon Muffins Recipe

STEP 1: Preheat oven to 350°F. Line or grease a 12-cup muffin tin. In a large bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.

STEP 2: In a separate bowl, combine discard, melted butter, brown sugar, eggs, vanilla, and milk. Mix until smooth.

STEP 3: Add the wet mixture to the dry ingredients and stir just until combined — don’t overmix.

STEP 4: Gently fold in chopped apples.

STEP 5: Fill the muffin pan ¾ of the way up with muffin batter.

STEP 6: Next make the crumb topping by combining flour, brown sugar, cinnamon, and salt. Add the cold butter and cut it into the dry ingredients with a pastry cutter or fork until the mixture becomes crumbly. Sprinkle the crumble on top of the muffin dough.

STEP 7: Bake for 20–25 minutes, or until a toothpick comes out clean.

STEP 8: Let cool in the pan for 5 minutes, then transfer to a rack to cool completely.
Tips for the Sourdough Apple Muffins
- These freeze well! You can wrap individually for an easy grab-and-go breakfast or I just simply place them in a gallon sized freezer safe Ziploc baggie once they've cooled.
- Try mixing in chopped pecans, shredded coconut, or raisins (one of our favorite add-ins!)for variation.
- This recipe works great with tart apples like Granny Smith or Honeycrisp.
More Sourdough Discard Recipes

The Best Sourdough Discard Apple Fritters Recipe

Apple Cinnamon Sourdough Discard Muffins Recipe
Ingredients
Dry Ingredients
- 2 cups (240g) all-purpose flour or fresh milled wheat
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- ½ teaspoon salt
- 1 ½ teaspoons cinnamon
- ½ teaspoon nutmeg
Wet Ingredients
- 1 cup sourdough starter discard or active sourdough starter
- ¾ cup (150g) light or dark brown sugar to be mixed with wet ingredients
- ½ cup melted unsalted butter
- 2 large eggs
- 1 ¼ cups milk
- 1 teaspoon vanilla extract
Add-Ins
- 1 ¼ cups finely chopped crisp apples peeled or unpeeled
Crumble Topping:
- ½ cup all-purpose flour
- ½ cup brown sugar packed
- ½ teaspoon ground cinnamon
- ¼ teaspoon salt
- ¼ cup cold unsalted butter cubed
Instructions
- Preheat oven to 350°F. Line or grease a 12-cup muffin tin.
- In a large bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, and nutmeg.
- In a separate bowl, combine discard, melted butter, brown sugar, eggs, vanilla, and milk. Mix until smooth.
- Add the wet mixture to the dry ingredients and stir just until combined — don’t overmix.
- Gently fold in chopped apples.
- Fill the muffin pan ¾ of the way up with muffin batter.
- Next make the crumb topping by combining flour, brown sugar, cinnamon, and salt. Add the cold butter and cut it into the dry ingredients with a pastry cutter or fork until the mixture becomes crumbly. Sprinkle the crumble on top of the muffin dough.
- Bake for 20–25 minutes, or until a toothpick comes out clean.
- Let cool in the pan for 5 minutes, then transfer to a rack to cool completely.
Notes
- These freeze well! You can wrap individually for an easy grab-and-go breakfast or I just simply place them in a gallon sized freezer safe Ziploc baggie once they've cooled.
- Try mixing in chopped pecans, shredded coconut, or raisins (one of our favorite add-ins!)for variation.
- This recipe works great with tart apples like Granny Smith or Honeycrisp.
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