These sourdough pumpkin muffins are soft, full of warm spices, and topped with buttery crumble—the perfect grab-and-go snack or cozy bake to share. Whether you enjoy them fresh from the oven or pull a batch from the freezer on a busy morning, they’re a treat you’ll want to make on repeat all fall long.
There’s something special about stocking the kitchen with seasonal treats once the crisp air of the fall season rolls in. Muffins, in particular, have always been one of my go-to bakes—quick and easy to whip up, endlessly versatile, and always welcome as a breakfast or snack. And when it comes to autumn flavors, these easy sourdough pumpkin muffins with a buttery crumble topping truly shine as the perfect fall treat.
Warm, spicy, and full of cozy flavors, they strike the right balance between comfort food and a nourishing bake you can feel good about. Muffins are the kind of thing that last year I found myself making over and over again, and this recipe has quickly become one of my favorite flavors to revisit.
What is a Sourdough Discard Recipe?
If you’re new to baking with sourdough, you may have heard about “discard.” A sourdough discard recipe is simply any bake that uses unfed starter, rather than relying on yeast or active fermentation for rising power. The leavening comes from baking powder and baking soda, while the sourdough starter plays a different role: it helps ferment the flour and brings depth of flavor, along with nutritional benefits.
Why use starter in muffins? The active sourdough starter, even when it’s a bit past its peak, provides:
- Health benefits – partial fermentation makes grains easier to digest.
- Added flavor and depth – that subtle tang balances the sweetness beautifully.
For best results, use a starter that’s been fed within the last week and stored in the fridge. This keeps the taste mild and prevents an overly acidic flavor in your muffins.
A Note on Fresh-Milled Flour
This recipe is very flexible when it comes to flour. You can make it with all-purpose flour (sometimes referred to as purpose flour) or whole wheat, or a combination of the two. If you mill your own flour, you’ll be glad to know this recipe works well with any wheat:
- Spelt lends a nutty flavor.
- Einkorn is an ancient grain with wonderful digestibility.
- Soft white wheat has the mildest taste, perfect for muffins with a delicate crumb.
No adjustments are needed—just swap the flour as you like. That’s the best part about this sourdough pumpkin muffin recipe: it’s endlessly versatile.
Ingredients Matter
Butter
- Pro Tip: I don’t believe in unsalted butter. I just don’t. I’m sorry but you’ll never convince me otherwise. Butter doesn’t taste like butter without the salt, and I want to taste the butter.
Pumpkin Puree
- Whether canned or homemade, pumpkin puree adds moisture as well as beautiful fall flavor.
Large Eggs
Vanilla
- Always use pure vanilla if possible!
Maple Syrup
- Natural sweeteners work really well in muffin recipes, and the buttery flavor of maple syrup perfectly complements this recipe. You could also use honey or brown sugar if preferred.
Sourdough Starter
- This is a sourdough recipe, after all 🙂 Fermented baked goods have a fuller flavor profile that is hard to put your finger on. But once you get used to it, it’s hard to go back.
Flour
- Muffins are so versatile and work with just about any flour you throw at them. I love using whole wheat flour for a heartier breakfast pastry.
Baking Powder and Baking Soda
- Your leavening agents.
Salt
- So important! Embrace it and love it.
Tips for Perfect Sourdough Pumpkin Muffins
- Use a large mixing bowl for the wet ingredients and a medium bowl or small bowl for the dry ingredients before combining.
- A Danish whisk is the perfect tool for making muffins! However, you can also use a wooden spoon.
- After mixing all of the ingredients together, cover and allow your batter to sit for 4-12 hours to ferment at room temperature or place it in the fridge overnight. As the batter ferments, you’ll see it start to puff up and bubbles will begin to form. This means you’re ready to bake!
- Line your muffin tin or muffin pan with paper muffin liners or tulip cupcake liners.
- Pro Tip: The tall, tulip cupcake liners allow you to really pile on the crumble topping without worrying about overflow. I love tulip liners because the muffins look consistent and a little fancy! I’ve been using these for years and I love them.
- Once baked, transfer your muffins to a wire rack to cool completely.
Storage
These sourdough pumpkin muffins store beautifully. Keep them in an airtight container on the counter for 2–3 days. For longer storage, wrap them in plastic wrap and place them in a freezer-safe bag or freezer bag. They reheat beautifully, which makes them perfect for meal prep or having on hand throughout the week.
Affiliate Note
Full disclosure: This post contains affiliate links, which means I may earn a small commission at no extra cost to you if you purchase through them. Thank you for supporting my kitchen experiments and seasonal bakes!
Sourdough Pumpkin Muffins with Brown Sugar Crumble
Ingredients
Muffins
- 170 g melted butter
- ½ cup pumpkin puree not pumpkin pie filling
- 100 g sourdough starter
- 320 g maple syrup
- 4 large eggs
- 1 tsp pure vanilla extract
- 260 g all-purpose flour whole wheat, or a combination
- 2 tsp baking powder
- ½ tsp baking soda
- 1 tsp salt
- 2 tsp cinnamon
- 1 cup chocolate chips or mini chocolate chips optional
Crumble
- 120 g flour
- 200 g brown sugar or substitute white sugar
- ½ tsp salt
- 1 tsp cinnamon or pumpkin spice
- 6 tbsp melted butter
Instructions
- Preheat oven to 350°F (175°C). Line a muffin pan with muffin cups, paper muffin liners, or cupcake liners.
- In a large bowl, whisk together the dry ingredients: flour, baking powder, baking soda, salt, and cinnamon.
- In a large mixing bowl, combine the wet ingredients: melted butter, pumpkin puree, sourdough starter, maple syrup, eggs, and vanilla extract. A whisk works well, though a stand mixer or hand mixer can make it even quicker.
- Pour the wet ingredients into the bowl of dry ingredients. Stir gently until a thick muffin batter forms. Fold in chocolate chips if using.
- Cover your batter and allow it to sit and ferment at room temperature for 4-12 hours. Alternately, you can place it in the fridge overnight. The batter will start to look puffed up and bubbles will begin to form.
- Make the crumble topping: In a small bowl, combine flour, brown sugar, salt, and cinnamon. Use a fork to stir in the melted butter until a crumbly texture forms.
- After finished fermenting, scoop batter into the prepared muffin tin using a ⅓ cup measure or large cookie scoop. Top generously with crumble. Note: The crumble is optional and is unfermented. If you're sensitive to gluten and only tolerate fermented grains, just leave the crumble off.
- Bake for 22–25 minutes, or until a toothpick inserted in the center comes out clean.
- Cool the baked muffins in the muffin pan for 5 minutes, then transfer to a wire rack.
I made these today and my family all said it’s the best muffin they’ve ever had!
So glad you enjoyed them!
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Thank you!