Sourdough Apple Muffins

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These sourdough apple muffins are soft, moist, and bursting with fresh apple flavor, topped with a buttery oat crumble. The combination of tangy sourdough starter discard, sweet crisp apples, and warm cinnamon makes these muffins perfect for cozy mornings or an afternoon snack.

Sourdough apple muffins on a cooling rack.

If you’re like me and love sourdough discard recipes, this one is a really great way to use your discard and enjoy a little taste of fall—any time of the year!

This simple recipe for sourdough apple cinnamon muffins is likely to become a family favorite. They bake up fluffy inside, with golden brown tops and a satisfying crunch from the crumble. Best of all, they’re easy to make with pantry staples and just a few fresh apples.

Sourdough apple muffins are a great addition to fall sourdough recipes, along with sourdough apple dumplings, sourdough apple cinnamon scones, sourdough pumpkin scones, and sourdough pumpkin pie!

A pile of sourdough apple muffins with one muffin cut in half to see the inside.

Why You’ll Love This Recipe

Great way to use sourdough discard: Perfect for those days you’re feeding your starter and don’t want to waste it.
Full of warm cinnamon flavor: The combination of cinnamon, nutmeg, and brown sugar makes them irresistible.
Make-ahead friendly: Store in an airtight container and rewarm for quick breakfasts or snacks.
Customizable: Add nuts, swap apples for pears, or try a mix of flours like all-purpose flour and whole wheat flour.

Ingredients

Find the full list of ingredients, amounts, and instructions in the recipe card at the bottom of this post.

Sourdough Discard: Adds a subtle tangy flavor and moisture while reducing food waste. You can also use an active sourdough starter.
Fresh Apples: Choose crisp apples like Honeycrisp, Fuji, or Gala for the best flavor and texture.
Brown Sugar: Gives the muffins a warm sweetness and helps create a soft, moist crumb.
All-Purpose Flour: Using all-purpose flour creates a fluffy muffin texture.
Cinnamon and Nutmeg: Warm spices that pair perfectly with apples, adding cozy flavor to every bite.
Butter: Adds richness and moisture for a soft and flavorful muffin.

Equipment

How to Make Sourdough Apple Muffins

Here are the step-by-step instructions for making sourdough apple muffins.

Step 1: Prepare the Muffin Batter

Preheat your oven to 425°F. Line a muffin tin with muffin liners.
In a large mixing bowl, whisk together the flour, baking powder, cinnamon, nutmeg, salt, and baking soda (Photo 1). This is your dry mixture—set it aside.
In a separate large bowl, cream the softened butter and brown sugar together with a hand mixer until light and fluffy (Photo 2).
Add the sourdough discard and mix until combined (Photo 3).
Stir in the sour cream and vanilla extract (Photo 4).
Beat in the eggs, one at a time, mixing well after each addition (Photo 5).
Add half of the dry ingredients to the wet ingredients and mix until just combined (Photo 6).
Add the remaining dry ingredients along with the diced apples (Photo 7). Stir gently until everything is well combined and the apples are coated with batter. A Danish dough whisk, spatula, or mixing spoon works well for this step (Photo 8).

Collage of four photos showing steps 5-8 for how to make sourdough apple muffins.

Step 2: Fill the Muffin Pan

Use a large cookie scoop to portion the muffin batter evenly into the prepared muffin cups (Photo 9).

Step 3: Make the Crumble

In a small bowl, combine the flour, oats, light brown sugar, cinnamon, and a pinch of salt.
Pour in the melted butter and stir until the mixture resembles wet sand (Photo 10).
Sprinkle the crumble mixture generously over each muffin (Photo 11).

Collage of four photos showing steps 9-12 for how to make sourdough apple muffins.

Step 4: Bake

Bake at 425°F for 5 minutes to create a high rise.
Without opening the oven door, reduce the heat to 350°F and continue baking for 15–18 minutes, or until a toothpick inserted into the center comes out clean.
Let the muffins cool in the pan for about 5 minutes (Photo 12), then transfer them to a wire rack to cool completely.

12 sourdough apple muffins on a wire cooling rack after baking.

How to Store

Store muffins at room temperature in an airtight container for up to 2 days.
For longer storage, refrigerate for up to 5 days.
To refresh, warm in the microwave or air fryer for a few seconds until soft, or put them in a 350 degree oven to warm.

Tips for Success

Don’t overmix the batter—this keeps the muffins tender.
Use crisp apples like Honeycrisp, Fuji, or Gala for the best flavor and texture.
For added crunch, mix chopped pecans or walnuts into the crumble.
Chop apples into small pieces or shred them for a different texture.
These muffins pair perfectly with coffee (they’d be great with homemade pumpkin spice lattes), tea (try my London fog tea latte recipe or my chai spice mix), smoothies, or apple cider.
Try serving with a drizzle of maple syrup or honey for extra sweetness.

Recipe Frequently Asked Questions

Can I use whole wheat flour?

Yes! You can replace up to half of the all-purpose flour with whole wheat flour for a heartier muffin.

Do I have to use sourdough discard?

You can use an active starter or discard—both work well in this sourdough muffin recipe. Discard will give a slightly tangier flavor.

Can I freeze these muffins?

Yes! Wrap each muffin individually in plastic wrap, then place in a freezer-safe bag. Thaw at room temperature or warm gently before serving.

What’s the best apple for baking muffins?

Any firm, fresh apples that hold their shape when baked will work. Honeycrisp, Granny Smith, and Fuji are all great options.

Should I peel apples for apple muffins?

It’s up to you. Peeling the apples creates a softer texture and blends seamlessly into the muffin, while leaving the peel on adds extra fiber and a bit of color. If your apples have thin, tender skin, you can skip peeling.