My Sourdough Apple Muffins are soft, cinnamon-topped, and bursting with juicy apple chunks in every bite. They’re the perfect cozy muffin to make when you’ve got sourdough discard and fresh apples on hand.
You can whip up these muffins in just a few bowls, no mixer needed, and they bake up golden and fluffy with slightly crisp tops. The subtle tang from the discard pairs beautifully with the warm spices and tender apples.
These muffins are perfect for fall mornings with hot coffee, but they’re just as good year-round. Bake them for back-to-school breakfasts, weekend brunches, or a cozy addition to your Thanksgiving bread basket.
They also make a thoughtful treat to drop off for a neighbor, bring to a potluck, or stash in the freezer for busy weeks. Anytime you want something warm, lightly spiced, and comforting, these muffins are a win.
If you enjoy these Sourdough Apple Muffins, you’ll love my Sourdough Banana Muffins, Sourdough Zucchini Muffins, and Sourdough Pumpkin Cream Cheese Swirl Muffins too. Each one is tender, moist, and packed with seasonal flavor.
If you're a chocolate lover like me, my Sourdough Chocolate Muffins are for you!
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Ingredients
For the muffins
- all-purpose flour
- baking powder
- baking soda
- kosher salt
- cinnamon
- nutmeg
- brown sugar
- granulated sugar
- sourdough discard, unfed
- neutral oil
- eggs
- vanilla extract
- whole milk or buttermilk
- peeled and finely chopped apples
Optional cinnamon sugar topping
- granulated sugar
- cinnamon
See recipe card for quantities.
Four-Step Overview
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.
Substitutions
Need to make a swap? Try these:
- Milk: Use dairy free milk
- Butter: Coconut oil or vegetable oil can be used instead of melted butter. A melted non-dairy butter would work great as well.
- Apples: Pears work well in place of apples.
- Cinnamon: Try pumpkin pie spice instead of cinnamon if you’re out.
Variations
Switch things up with these easy muffin twists:
- Nuts: Add ½ cup chopped toasted walnuts or pecans for crunch.
- Whole wheat: Swap half the all-purpose flour for whole wheat flour.
- Shredded Apple: Use shredded apple instead of diced for a more even texture.
- Berries: Stir in a handful of raisins or dried cranberries for a little chew.
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
- Wire cooling rack
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. Streusel will soften quickly when stored.
To freeze, wrap tightly in plastic wrap 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.
Audrey's Tip
That initial 5 minutes at 425°F gives you those bakery-style domes! Don’t skip it. For extra crunch, sprinkle coarse sugar or cinnamon sugar generously before baking
Related
Looking for other recipes like this? Try these:
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.
- 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.
- 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.
- 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.