These Sourdough Apple Muffins are a delightful fusion of tangy sourdough and sweet apples, creating a moist and flavorful treat that's perfect for breakfast or a midday snack.

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These sourdough apple cinnamon muffins are soft, sweet, and full of cozy fall flavor. They're made with sourdough discard, which gives them a light tang and helps cut down on food waste.
Fresh grated apples, cinnamon, and brown sugar make these muffins taste just like your favorite apple dessert, but in an easy grab-and-go form.
Whether you're trying to use up leftover sourdough starter or just love apple-flavored treats, this Sourdough Apple Muffins recipe is a simple and tasty choice. Add the crumb topping for extra crunch, and you've got a bakery-style muffin right from your own kitchen!
Jump to:
- 💛 Why You'll Love This Recipe
- 🛒 Ingredients
- 🔀 Substitutions & Variations
- 💰 Budget-Friendly Tips
- 🥄 Instructions for Sourdough Apple Muffins
- ⏳ Long-Fermented Sourdough Apple Muffins
- 👩🏻🍳 Expert Tips
- ❄️ Storage, Reheating & Make Ahead
- 🥗 Side Dishes or Pairing Ideas
- ❓ Sourdough Apple Muffins FAQs
- 🍽️ More Recipes You'll Love
- 📖 Recipe
- 💬 Comments
💛 Why You'll Love This Recipe
- Great way to reduce waste - Using sourdough discard in these muffins means you're not throwing out perfectly good starter. It's an easy and delicious way to make your sourdough baking more sustainable.
- Flavorful twist on a favorite - These Sourdough Apple Muffins are a tasty adaptation of my popular Sourdough Discard Banana Muffins. The apples and cinnamon give them a cozy fall flavor, while the sourdough adds depth and moisture.
- Bakery-style texture - Thanks to the Greek yogurt and melted butter, these muffins turn out soft and fluffy with a tender crumb. The optional crumb topping adds just the right amount of crunch.
🛒 Ingredients

Apples - Freshly grated apples add natural sweetness and keep the muffins moist. You can use any apple you have on hand, but baking apples like Granny Smith, Honeycrisp, Fuji, or Braeburn hold up better and give the muffins more flavor and texture.
Sourdough Discard - This adds a slight tang and deeper flavor without needing your sourdough starter to be bubbly or active. Don't have discard? You can also use active sourdough starter, both work great in this recipe.
Greek Yogurt - Greek yogurt helps make the muffins soft, moist, and rich. I used plain nonfat Greek yogurt, but full-fat or vanilla yogurt works too. You can also swap it for sour cream or a thick plant-based yogurt if needed.
See the recipe card below for full ingredients and instructions.
🔀 Substitutions & Variations
Yogurt or Sour Cream: You can swap Greek yogurt for sour cream or a thick plant-based yogurt for a dairy-free option. Both give your muffins the same moist, rich texture.
Butter or Oil: Melted butter adds depth and flavor, but vegetable oil, canola oil, or melted coconut oil work great too if that's what's in your pantry.
Brown Sugar: Light or dark brown sugar both work perfectly. For a more natural option, use coconut sugar or even a mix of white sugar and molasses.
Flour Options: These muffins are flexible! All-purpose flour gives the lightest texture, while white whole wheat flour adds a subtle nuttiness and more fiber. You can also try a 50/50 mix for balance, it still bakes up soft and fluffy.
Spices: For extra fall flavor, add ¼ teaspoon each of ground ginger, nutmeg, or cloves along with the cinnamon.
Add-Ins:
- Nuts: Add up to 1 cup of chopped walnuts, pecans, or almonds for crunch.
- Dried Fruit: Stir in raisins, cranberries, or chopped dates for natural sweetness.
- Chocolate Chips: Add mini or white chocolate chips for a dessert-like version.
- Shredded Coconut or Carrots: Adds extra texture and moisture-great for sneaking in veggies!
💡 Tip: Keep total add-ins around 1 cup so your muffins stay light and fluffy instead of dense.
💰 Budget-Friendly Tips
Use what's in season: Apples are most affordable in fall, but this recipe works beautifully with any firm, budget-friendly apple you have on hand, or even a mix of varieties.
Stretch your ingredients: Grate the apples (instead of dicing) to spread flavor and moisture through the whole batch, making your muffins taste more indulgent without using extra fruit.
Simple swaps: Substitute oil for butter and use store-brand yogurt or sour cream to cut costs while keeping the texture moist and tender.
🥄 Instructions for Sourdough Apple Muffins
Step 1: Preheat oven to 425°F. Line a muffin tin with paper liners or lightly grease.

Step 2: In a large bowl, add sourdough discard, Greek yogurt, melted butter, brown sugar, vanilla, and egg. (Image 1). Whisk together until smooth. (Image 2).
Step 3: Grate and add the apples to the wet mixture. (Image 3). Stir together well to incorporate. (Image 4).

Step 4: In another bowl, add the flour, baking powder, baking soda, salt, and cinnamon. (Image 5). Whisk together until combined. (Image 6).
Step 5: Add the dry mixture to the wet mixture. (Image 7). Gently fold dry ingredients into wet until just combined. Don't overmix! (Image 8).

Step 6: In a small bowl, add the topping ingredients, flour, brown sugar, cinnamon, and cubed cold butter. (Image 9). Mix together until crumbly.
Step 7: Divide batter among 12 muffin cups. (Image 10). Top with crumble topping. (Image 11).
Step 8: Bake at 425°F for 5 minutes, then reduce to 350°F (without opening the oven) and bake for another 16-18 minutes. (Image 12).
Step 9: Let muffins cool in pan for 5 minutes, then move to a wire rack to cool completely.
Enjoy!
⏳ Long-Fermented Sourdough Apple Muffins
For a deeper flavor and easier digestion, try a long fermentation. This allows the sourdough culture to gently break down the flour, creating soft, tangy muffins that are easier on your stomach.
How to Long Ferment:
- Mix: In a large bowl, combine sourdough discard, melted butter, Greek yogurt, and flour until fully incorporated.
- Ferment: Cover and rest at room temperature for 8-12 hours to let the natural fermentation develop flavor.
- Finish: Add grated apples, brown sugar, egg, vanilla, baking powder, baking soda, salt, and cinnamon. Stir just until combined.
- Bake: Follow the original baking directions.
Tips: If the batter thickens too much after fermenting, stir in a splash of milk or water. For a stronger sourdough tang, ferment up to 24 hours, but note the flavor will be more pronounced.
👩🏻🍳 Expert Tips
- Scaling: Double the recipe to make 24 muffins for a crowd or freeze extras for grab-and-go breakfasts.
❄️ Storage, Reheating & Make Ahead
Storage: Store muffins in an airtight container at room temp for up to 3 days, or refrigerate for up to a week. They also freeze beautifully, just pop them into a freezer bag and store for up to 3 months.
Reheating: Warm up a muffin in the microwave for 15-20 seconds or in a toaster oven for that fresh-from-the-oven feel.
Make-Ahead: You can mix the dry ingredients and wet ingredients separately and refrigerate overnight. Combine them in the morning and bake fresh!
🥗 Side Dishes or Pairing Ideas
These Sourdough Apple Muffins make a wonderful addition to any breakfast or brunch spread. Serve them warm with butter, apple butter, or a drizzle of honey for a simple morning treat.
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❓ Sourdough Apple Muffins FAQs
Nope! These muffins are a quick bread recipe, so there's no need to ferment the batter. You can mix and bake them right away. Perfect for a fast sourdough discard solution.
Yes! Active starter will work just fine in this recipe. It may add a little more rise and a slightly stronger tang, but the muffins will still turn out delicious.
The two-step baking process helps create a perfect muffin texture. The initial 5 minutes at a higher temperature (425°F) gives the muffins a nice rise and a slightly golden top.
After that, lowering the temperature to 350°F helps them bake all the way through without drying out. This method results in a soft, tender muffin with a slightly crisp top and perfectly cooked interior.

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🐝 If you tried this Sourdough Apple Muffins, please leave a ⭐️ star rating and share your buzz in the 💬 comments below. I'd truly appreciate it!
📖 Recipe
Sourdough Apple Muffins
Ingredients
- ½ cup sourdough starter discard, unfed (120g) - ($0.15)
- ¼ cup Greek yogurt (60g) - ($0.27)
- 6 tablespoons butter, melted (85g) - ($0.74)
- ¾ cup brown sugar, packed (150g) - ($0.71)
- 2 teaspoons vanilla extract - ($0.04)
- 1 large egg - ($0.37)
- 1 ½ cups apples, grated (150g) - ($1.72)
- 2 cups all-purpose flour (160g) - ($0.25)
- 2 teaspoon baking powder - ($0.08)
- 1 teaspoon baking soda - ($0.01)
- ½ teaspoon salt - ($0.01)
- 1 teaspoon ground cinnamon - ($0.08)
- ½ teaspoon ground nutmeg - ($0.04)
Crumb Topping
- ⅓ cup all-purpose flour - ($0.04)
- ¼ cup brown sugar - ($0.31)
- ¼ teaspoon ground cinnamon - ($0.02)
- 2 tablespoons butter, cold and cubed - ($0.25)
Instructions
- Prep. Preheat the oven to 425°F. Line a muffin tin with liners or lightly grease.
- Mix the wet ingredients. In a large bowl, whisk together the sourdough discard, Greek yogurt, melted butter, brown sugar, vanilla, and egg until smooth.
- Add apples. Stir the grated apples into the wet mixture until evenly distributed.
- Mix the dry ingredients. In a separate bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
- Combine. Gently fold the dry ingredients into the wet mixture just until combined. Do not overmix.
- Make the crumb topping. In a small bowl, mix the flour, brown sugar, cinnamon, and cold butter until crumbly.
- Assemble. Divide the batter evenly among 12 muffin cups and sprinkle the crumb topping over each.
- Bake. Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F without opening the door. Continue baking for 16-18 minutes, until a toothpick inserted in the center comes out clean.
- Cool. Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
Notes
- Avoid overmixing. Stir just until combined to prevent dense muffins.
- Apple tips. Use firm apples and grate them finely for even moisture.
- Ingredient swaps. Sour cream or plant-based yogurt can replace Greek yogurt. Oil can replace butter if needed.
- Add-ins. Up to 1 cup chocolate chips or chopped nuts may be added.
- Fermented option. Mix discard, yogurt, butter, apples, and flour. Cover and rest 8-12 hours, then add remaining ingredients and bake.
- Storage. Store at room temperature for 3 days, refrigerate up to 1 week, or freeze up to 3 months.
Nutritional Information
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Nicole Durham says
From the crunchy exterior to the soft apple muffin inside, we absolutely can not get enough of these sourdough muffins!