Sourdough Discard Apple Muffins with Cinnamon Streusel

These sourdough discard apple muffins are soft, warmly spiced, and topped with a buttery cinnamon streusel. A cozy, from-scratch recipe that’s perfect for using up extra starter and welcoming the flavors of fall!

Every fall, our family marks the season with a trip back to Western North Carolina for apple picking. The crisp air, rolling hills, and sweet crunch of fresh apples bring back memories year after year. And once we get home with a basket full of apples? It’s time to bake.  We bring home a variety of fresh apples and make everything from easy apple crisp to apple turnovers.

One of my favorite ways to use both fresh apples and sourdough discard is with these Sourdough Discard Apple Muffins with Cinnamon Streusel. They’re moist, tender, and layered with cozy fall flavors—like cinnamon, brown sugar, and buttery apples. The crowning touch is a golden, crumbly streusel topping that bakes to perfection.

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What You’ll Love About These Muffins

• A delicious way to use up sourdough discard–I love finding creative ways to use up discard, because I don’t like seeing things go to waste–especially food!  Everyone enjoys a good muffin!
• Filled with warm fall spices and juicy apple bits–I love what the spices and apple flavor does to this recipe, making it the perfect fall recipe.
• Topped with a bakery-style cinnamon streusel–The best part of a muffin is always the top of the muffins, so not why not make it more indulgent by adding a little streusel!
• Can be made ahead and frozen–One of my favorite things about baking muffins and baked goods, is that so many of these recipes can be made ahead and frozen.  Always helps me out in a pinch or when I need a little something special for the family for breakfast!
• Kid-friendly and great for snacks or breakfast–Muffins are always great for breakfast or for snacks!  I love that this kind of snack is made from my home and is filled with goodness! 

Key Ingredients

• Apples – I used Pink Lady apples because they’re crisp, slightly tart, and hold up beautifully when baked. That said, any firm, flavorful apple will work—choose your favorite or whatever you have on hand.  The apple flavor tends to still come through no matter the kind you use.
• Cinnamon – The warm cinnamon spice is essential for giving the muffins their classic fall flavor. It adds depth and a comforting aroma that pairs perfectly with the apples.
• Sour Cream – A secret weapon for tender muffins, sour cream adds richness and moisture without making the batter too heavy. It also gives the muffins a subtle tang that enhances the flavor of the sourdough discard.

You can find a full list of ingredients in the recipe card located at the bottom of this post.

How to make Sourdough Apple Cinnamon Muffins

Start by prepping your muffin pan—either line it with paper liners or lightly grease it. Then, in a large bowl, whisk together your dry ingredients: all purpose flour, baking powder, baking soda, salt, cinnamon, and brown sugar. This base gives your muffins structure and the perfect hint of spice.

In a separate bowl, mix together your wet ingredients: melted butter, sourdough discard (straight from the fridge is fine!), eggs, sour cream, and vanilla extract. The discard adds depth and moisture, while the sour cream brings a rich, tender crumb.

Combine the wet and flour mixture, being careful not to overmix. Then fold in your apples to the muffin batter. I love using Pink Lady apples for their balance of tart and sweet, but you can use Honeycrisp, Granny Smith, or whatever fresh variety you have on hand.

Now for the streusel: mix flour and brown sugar in a small bowl, then stir in melted butter with a fork until crumbly. Spoon the batter into muffin cups (or use muffin liners), top with the streusel, and for best results gently press it into the tops so it sticks during baking.

Start the muffins at a higher temperature (400°F) for five minutes to help them rise, then reduce the oven to 350°F to finish baking evenly and slightly golden brown.  When they are done let them cool in the muffin tin or on a wire rack for a few minutes before serving.

Tips & Variations

• No streusel? Sprinkle the tops with turbinado sugar for crunch.
• Love glaze? Mix powdered sugar with a splash of milk for a sweet drizzle.
• No cinnamon? Sub in apple pie spice for a warmer blend.

Storage & Make-Ahead

Let the sourdough apple muffins cool completely before storing in an airtight container. They’ll keep at room temperature for 2–3 days. For longer storage, freeze in a single layer before transferring to a freezer-safe bag—they’ll last up to 2 months. Reheat in the oven or let them thaw at room temp.

Recipe FAQs

These sourdough discard apple muffins are the kind of cozy, comforting perfect muffin that brings everyone to the table—whether it’s for a slow weekend breakfast, an after-school snack, or just a treat to share with neighbors–it’s a great way to bring people together. So grab those apples, use up that discard, and enjoy a taste of fall in every bite of these apple cinnamon sourdough muffins!

More Cozy Fall Recipes

• Sourdough Blueberry Muffins with Crumb Topping
• Bakery Style Sourdough Discard Muffins (Master Recipe)
• Best Sourdough Banana Muffins with Walnut Crumb Topping

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If you make this recipe, please leave a rating on the recipe card below! I’d also love for you to tag me @autumn.chasingoursimple on Instagram so I can see what you’ve been baking!