My sourdough apple muffins are soft, cinnamon-topped, and bursting with juicy apple chunks in every bite.
The subtle tang from the discard pairs beautifully with the warm spices and tender apples. If you love using up discard in muffins, you'll also enjoy my sourdough discard banana muffins, sourdough double chocolate muffins, and my sourdough zucchini muffins.
Quick Look: Sourdough Apple Muffins
⏱️ Ready In: About 40 minutes
🔥 Bake Time: About 20 minutes (5 min at 425°F, then 15–18 min at 350°F)
🍽️ Makes: 12 muffins
✨ Calories: Approximately 270 per muffin
🥄 Main Ingredients: Fresh apples, sourdough discard, warm spices, cinnamon sugar topping
🌿 Dietary Info: Vegetarian (easily dairy-free)
💛 Why You'll Love It: Soft, bakery-style apple muffins with tall domes, a cinnamon sugar top, and a great use for your discard.
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Why You'll Love This Recipe
- A perfect use for sourdough discard. It adds moisture and a subtle tang that plays beautifully with apples, the same way it does in my sourdough discard blueberry muffins.
- Loaded with fresh apple. Juicy apple chunks in every bite.
- Bakery-style domes. A hot-oven start gives you those tall, crackly tops.
- No mixer needed. Just a couple of bowls and a whisk.
- Cozy and versatile. Lovely for fall mornings or year-round, like my sourdough pumpkin cream cheese muffins and my apple oat muffins.
Jump to:
- Quick Look: Sourdough Apple Muffins
- Why You'll Love This Recipe
- Ingredients
- Easy Substitutions & Variations
- How to Make Sourdough Apple Muffins
- Expert Tips
- What Makes This Recipe Special?
- Sourdough Apple Muffins FAQs
- Sourdough Apple Muffins Troubleshooting Guide
- Sourdough Apple Muffin Storage
- Other Sweet Breakfast Recipes to Consider
- Sourdough Apple Muffins
Ingredients
- All-purpose flour: The structure of the muffins.
- Baking powder + baking soda: Your lift for tall domes.
- Kosher salt: Balances the sweetness.
- Cinnamon + nutmeg: Warm fall spices.
- Brown sugar + granulated sugar: Brown sugar for moisture, granulated for balance.
- Sourdough discard (unfed): Adds moisture and a subtle tang — a great way to use it up, like my sourdough discard coffee cake.
- Neutral oil: Keeps the muffins soft for days.
- Eggs + vanilla: Bind and enrich the batter.
- Whole milk or buttermilk: Loosens the batter (buttermilk adds tang).
- Peeled, chopped apples: The star — Granny Smith or Honeycrisp work well.
- Cinnamon sugar topping (optional): For a crunchy, spiced finish.
See the recipe card for quantities.
Easy Substitutions & Variations
- Dairy-free: Use a non-dairy milk and a melted plant-based butter or neutral oil.
- Apples: Pears work well in place of apples.
- Spice swap: Use pumpkin pie spice in place of the cinnamon if you're out.
- Shredded apple: Use shredded apple instead of diced for a more even texture.
- Nuts: Add ½ cup chopped toasted walnuts or pecans for crunch.
- Whole wheat: Swap half the all-purpose flour for whole wheat.
- Dried fruit: Stir in raisins or dried cranberries for a little chew.
- More apple bakes: Try the same flavors in my apple pie cinnamon rolls.
- Chocolate lover? Swap the apple plan entirely for my sourdough double chocolate muffins.
How to Make Sourdough Apple Muffins
Note: I bake by weight for accuracy. Cup measurements are approximate and may vary depending on how you scoop.
Step 1: Mix the batter: Whisk wet ingredients, then fold in dry ingredients and apples.
I chopped my apples a bit larger for more texture in the muffins, but if you prefer a more uniform muffin, finely dice or shred the apples before mixing them into the batter.
Step 2: Fill the pan: Divide batter into muffin cups, filling almost to the top.
Note: In the next photo, you can see that I filled every other muffin liner spot, I did this to test if it would improve the spring and it did not. Feel free to fill all 12 muffin liners!
Step 3: Bake the muffins: Bake at 425°F for 5 minutes, then lower to 350°F and bake until set.
Step 4: Cool & enjoy: Cool slightly on a rack before serving warm.
Weigh your ingredients! Using a kitchen scale ensures your measurements are accurate, which is key for getting consistent results in baking. It takes the guesswork out of measuring and helps your recipes turn out exactly as intended every time.
Expert Tips
- Start with a hot oven. The initial 5 minutes at 425°F gives you those tall, bakery-style domes — don't skip it.
- Don't open the oven when you drop the temp. Keeping the heat steady helps the rise.
- Don't overmix. Fold just until combined for a tender crumb.
- Fill the cups almost full. Generously filled cups give the best dome.
- Add the cinnamon sugar before baking. Sprinkling it on the raw batter bakes it into a crunchy top.
What Makes This Recipe Special?
These muffins land squarely in bakery territory: fresh apple chunks in a soft, spiced crumb, a tall domed top from the hot-oven start, and a crunchy cinnamon sugar finish. The sourdough discard is the quiet hero — it adds moisture and a subtle tang that keeps them from tasting flat, plus it's a delicious way to use up what you'd otherwise toss.
If you love a cozy, fall-spiced bake, you're in good company on the blog. My easy apple pie crumb bars put the same apple-and-cinnamon flavor into a sliceable bar, and my sourdough pumpkin bread is another warm-spiced favorite.
Sourdough Apple Muffins FAQs
Granny Smith or Honeycrisp both work well — a tart-sweet apple holds its shape and balances the sweetness.
The original recipe uses peeled apples for the softest texture, but you can leave the skins on if you prefer a more rustic muffin.
Yes — this recipe works great with a non-dairy milk, and you can use oil or plant-based butter to keep it fully dairy-free.
Yes — active starter works in place of unfed discard.
Yes — wrap tightly and freeze for up to 2 months; thaw overnight in the fridge or warm in the microwave for 20–30 seconds.
Sourdough Apple Muffins Troubleshooting Guide
| Problem | Cause | Fix |
|---|---|---|
| Flat muffins, no dome | Batter overmixed or oven not hot enough to start. | Mix just until combined and start the bake at 425°F. |
| Dense, gummy crumb | Overmixed batter. | Fold gently and stop as soon as the flour disappears. |
| Apples sank | Apple pieces too large/heavy. | Dice smaller or toss apples in a little flour first. |
| Gummy center | Underbaked. | Bake until a toothpick comes out clean. |
| Topping slid off | Added after baking. | Sprinkle the cinnamon sugar on the raw batter before baking. |
Sourdough Apple Muffin Storage
- Let muffins cool completely before storing. Keep in an airtight container at room temperature for up to 3 days, or refrigerate for up to 5 days. (The cinnamon sugar topping softens as it sits.)
- To freeze, wrap tightly or store in a freezer-safe container for up to 2 months. Thaw overnight in the refrigerator or reheat in the microwave for 20–30 seconds.
Other Sweet Breakfast Recipes to Consider
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Sourdough Apple Muffins
Equipment
- Kitchen Scale
- 12-cup muffin tin
- 3-tablespoon cookie scoop (for scooping batter into the muffin liners)
- Parchment muffin liners or nonstick spray
- Medium mixing bowl
- Large mixing bowl
- Whisk
- spatula
- Measuring spoons
- Toothpick or cake tester
Ingredients
For the muffins:
- 250 g all-purpose flour 2 cups
- 1 ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon kosher salt
- 1 ½ teaspoon cinnamon
- ¼ teaspoon nutmeg
- 100 g brown sugar packed (½ cup)
- 75 g granulated sugar ⅓ cup
- 120 g sourdough discard unfed (½ cup)
- 120 ml neutral oil ½ cup
- 2 large eggs room temperature
- 1 teaspoon vanilla extract
- 120 ml whole milk or buttermilk ½ cup
- 150 g peeled and finely chopped apples 1 heaping cup; Granny Smith or Honeycrisp work well
Optional cinnamon sugar topping:
- 2 tablespoon granulated sugar
- ½ teaspoon cinnamon
Instructions
- Prep the oven & pan: Preheat oven to 425°F (220°C). Line a 12-cup muffin tin with parchment liners or grease well.
- Mix the dry ingredients: In a medium bowl, whisk together flour, baking powder, baking soda, salt, cinnamon, and nutmeg.250 g all-purpose flour, 1 ½ tsp baking powder, ½ tsp baking soda, ½ tsp kosher salt, 1 ½ tsp cinnamon, ¼ tsp nutmeg
- Make the batter: In a large bowl, whisk brown sugar, granulated sugar, oil, eggs, vanilla, sourdough discard, and milk until smooth. Gently fold in the dry ingredients until just combined, then fold in chopped apples.100 g brown sugar, 75 g granulated sugar, 120 g sourdough discard, 120 ml neutral oil, 2 large eggs, 1 tsp vanilla extract, 120 ml whole milk or buttermilk, 150 g peeled and finely chopped apples
- Fill & bake: Divide batter evenly into muffin cups, filling almost to the top for a tall rise. Sprinkle with cinnamon sugar if using. Bake at 425°F for 5 minutes, then reduce oven temperature to 350°F (175°C) and bake an additional 15–18 minutes, until a toothpick comes out clean.2 tbsp granulated sugar, ½ tsp cinnamon
- Cool & serve: Let muffins cool in the pan for 5 minutes before transferring to a wire rack. Best enjoyed warm!
Megan says
Could I use a nondairy milk?
Audrey says
Yes! You can definitely use a nondairy milk—this recipe works great with it. We’ve included it in the substitutions section if you need to substitute any other ingredients.