Apple Sourdough Muffins with Crumb Topping

If I could only bake one muffin recipe for the rest of my life, it would hands-down be these apple sourdough muffins.

I’m not exaggerating when I say: these are the best muffins I have ever eaten. Ever.

The texture is soft and fluffy, and the apples bring just the right balance of sweet and juicy with a hint of cinnamon spice, and that buttery crumb topping with the vanilla drizzle? It’s absolute magic!

This was one of those recipes that came together with one goal in mind: make something ridiculously delicious with my sourdough discard. And let me tell you, it did not disappoint.

Whether you’re brand new to baking with sourdough or looking for your next favorite muffin recipe, you are going to fall in love with these sourdough apple muffins!

This post may contain affiliate links. Please read our disclosure policy.

When I first started learning about sourdough, everyone seemed to be talking about discard crackers. Every time I searched “what to do with sourdough discard,” I got the same answer: crackers, crackers, crackers.

And listen, maybe I just haven’t found the one yet, but I still haven’t come across a discard cracker recipe I actually love, or like that for matter.

Meanwhile, no one was talking about amazing, delicious recipes like these apple sourdough muffins. Why aren’t we shouting from the rooftops that you can make soft, fluffy, flavor-packed muffins with your leftover starter? That’s when I made it my mission: to create seriously good sourdough discard recipes that you’ll actually want to make again and again.

And yes, I now intentionally overfeed my starter just so I have extra discard to make another batch of these sourdough apple cinnamon muffins. Totally worth it.

Why You’ll Love These Muffins

These apple sourdough muffins are the perfect combination of everything you love about baking. The texture? Light, fluffy, and oh-so-soft. And thanks to the sourdough discard, they come out extra tender and moist with that rich, bakery-style flavor that keeps you coming back for more. The sourdough magic works behind the scenes to make a really, really good muffin even better.

Not only are they delicious, but they also come together with ease. Whether you’re a seasoned baker or just starting out, this recipe is simple and totally approachable. Plus, the cinnamon-spiced apples add that classic apple pie flavor, and the crumb topping with the vanilla glaze? Let’s just say you’ll be licking your fingers and reaching for another before the first one’s gone.

One of my favorite things about this recipe (besides eating the muffins, obviously) is the way my kitchen smells while they’re baking. That mix of warm cinnamon, sweet apples, and buttery crumb topping? It’s unreal.

And honestly, nothing makes me smile more than opening the airtight container the next day and getting hit with that same amazing scent all over again. 

These apple sourdough muffins aren’t a total experience. Whether you’re baking them for a weekend breakfast, sharing with friends, or sneaking one for a midday snack, they hit the mark every time. And since they use sourdough discard, you get to turn something you’d normally toss into something you’ll want to bake on repeat.

Ingredients for Apple Sourdough Muffins with Crumb Topping & Vanilla Glaze

Here’s what’s going into the best apple sourdough muffins you’ll ever eat:

For the Muffins:

• All-purpose flour: the base that gives these muffins their perfect structure.
• Baking soda & baking powder: for that nice fluffy rise.
• Ground cinnamon: because apples and cinnamon are a match made in muffin heaven.
• Salt: just a pinch to balance out the sweetness.
• Unsalted butter: softened to room temperature for that rich, buttery flavor.
• Brown sugar: adds depth and softness to the muffins.
• Granulated sugar: for a bit of extra sweetness and structure.
• Eggs: they help bind everything and add moisture.
• Vanilla extract: for that warm, sweet flavor boost.
• Milk: any kind you like (just make sure it’s room temperature).
• Sourdough discard: adds moisture, softness, and a touch of flavor that makes these muffins really shine. For best flavor and texture, use sourdough discard that’s about 1–2 days old—just enough tang to balance the sweetness!
• Chopped apples: I like to use sweet, crisp varieties and cut them into small chunks so every bite has some apple goodness.

For the Crumb Topping:

• All-purpose flour: the base of the crumb.
• Brown sugar & white sugar: for that sweet, crunchy contrast.
• Ground cinnamon: gives the crumble a little extra warmth.
• Melted butter: brings it all together and helps the crumb crisp up beautifully in the oven.

For the Vanilla Glaze:

• Powdered sugar: the base of the glaze.
• Milk: just enough to make it drizzle-worthy.
• Melted butter: adds richness.
• Vanilla extract: for that sweet finishing touch.

Let’s Talk Apples: Choosing the Right Kind for the Best Flavor

For these muffins, I like to go with crisp apples that are naturally sweet, crisp, and hold their shape while baking. You want little juicy apple pockets in every bite. Not mushy chunks that disappear into the batter.

My go-to apples for this recipe are Honeycrisp, Pink Lady Apples, or Fuji. They’re sweet enough on their own, have a nice tartness to balance the sugar, and they keep that perfect bite after baking.

If you like a little more tang, Granny Smith apples work too. Just know you’ll get a slightly tarter result, which can be a fun contrast with the glaze and crumb topping.

Honestly, you can’t go too wrong here. Just steer clear of super-soft apples like Red Delicious. Save those for snacking, not baking.

How to Make Apple Sourdough Muffins

Step 1: Preheat the Oven & Prep Muffin Tin

Start by preheating your oven to 425°F (220°C) and lining your muffin pan with paper liners (or give it a quick spray with nonstick spray if you prefer). This ensures your muffins won’t stick and will come out of the tin easily.

Step 2: Mix Dry Ingredients

In a medium-sized bowl, whisk together the flour, baking soda, baking powder, cinnamon, and salt. Set this flour mixture aside for now.

Step 3: Cream Butter & Sugars:

In another large mixing bowl (or the bowl of a stand mixer), beat the softened butter with the brown sugar and granulated sugar until the mixture is light and fluffy (about 2 minutes on medium speed). This is your wet base, and trust me, it’s the start of some delicious things.

Step 4: Add Eggs, Vanilla, Milk and Sourdough Discard

Beat in the eggs, vanilla extract, milk and sourdough discard. Be sure that everything is fully combined.

Step 5: Combine Wet & Dry Ingredients

Gradually add the dry flour mixture to the wet ingredients, mixing just until combined. You don’t want to overwork the batter, or your muffins might turn out a little tough.

Step 6: Prepare and Fold in the Fresh Apples

Peel and chop your apples into small ½-inch chunks (you will need about 2 large apples). You want pieces that are big enough to stand out, but small enough to bake evenly into the muffins. Once your apples are prepped, gently fold them into the batter using a spatula or wooden spoon. Don’t rush it. Make sure they’re nice and evenly distributed so you get juicy apple bites in every single muffin.

Step 7: Make the Crumb Topping

In a small bowl, mix together the flour, brown sugar, white sugar, and cinnamon. Add the melted butter and stir until the mixture becomes crumbly. This is the perfect topping for those extra crunchy muffin edges!

Step 8: Fill Muffin Tin & Top With Crumb Topping

Using a large cookie scoop or spoon, scoop the muffin batter into the muffin cups, filling them almost full. Generously sprinkle the crumb topping on top of the muffins before popping them into the oven. Press the crumb topping down slightly into the muffins (just slightly so it sticks).

Step 9: Bake

Bake the muffins at 425°F for the first 5 minutes. This gives them that beautiful high rise. Without opening the oven door, reduce the temperature to 350°F and continue baking for another 18–22 minutes, or until a toothpick inserted into the center comes out clean. You’ll know they’re ready when the tops are golden brown and your kitchen smells incredible.

Step 10: Cool & Drizzle With Vanilla Glaze

Allow the muffins to cool in the tin for a 5 minutes, then transfer them to a wire rack to cool completely. Once they’re cool, make your vanilla glaze and drizzle over the muffins. The glaze adds a sweet, creamy finish that makes each bite melt-in-your-mouth perfection.

Back in university, I had a little cake business because I was obsessed with piping cakes. (Fun fact: my husband actually used that business as part of his sneaky proposal. But that’s a story for another day!) So now I’ve got piping bags all over the house, and I love using one to glaze these muffins. But don’t worry, a spoon works just as well for a classic drizzle.

How to Store & Freeze Your Sourdough Discard Apple Muffins

If you’re lucky enough to have leftovers (which might be a big if), these muffins will stay fresh for up to 3 days when stored in an airtight container at room temperature. For longer storage, you can freeze them! Just wrap each muffin tightly in plastic wrap or place them in a freezer-safe bag. When you’re ready to enjoy, place them on the counter and allow them to full thaw.

FAQs & Troubleshooting Tips

Can I use active starter instead of discard?
Yes! If you’ve got an active sourdough starter, you can use that in place of discard. Just be sure to account for the fact that it’s more active, so your muffins might rise a little faster.

Why did my muffins turn out tough?
Overmixing the batter is usually the culprit! When you add the dry ingredients, stir just until everything is combined. If you mix too much, you could end up with tough muffins.

Can I make these muffins ahead of time?
Yes! These muffins store well in an airtight container at room temperature for 2–3 days, or in the fridge for up to 5 days. You can also freeze them for longer storage. Just thaw at room temperature.

Can I skip the crumb topping or glaze?
You can, but I wouldn’t. Trust me, they’ll be irresistible with the crumb topping and vanilla glaze. It’s the finishing touch that takes these muffins from good to unforgettable.

Did you try this recipe? I’d love to see how it turned out! Leave a comment below and tag @catchthecrumbsourdough on Instagram to show it off!