Got a jar of sourdough discard staring at you from the fridge? These sourdough pumpkin muffins are exactly what to do with it — and they just might become your new favorite fall recipe!

Close up of a sourdough pumpkin muffin with crumble topping showing moist texture and tall bakery-style dome - Hostess At Heart

They’re incredibly moist, packed with warm pumpkin spice flavor, and topped with a sweet, buttery crumble that makes them taste like they came from a fancy bakery. The best part? You can whip up a batch in just 35 minutes, and they’re perfect for breakfast, snack time, or even dessert.

If you’ve been feeding your sourdough starter and wondering what to do with all that extra discard, this pumpkin muffin recipe is your answer. The sourdough adds a subtle tangy flavor that perfectly balances the sweetness of the pumpkin and brown sugar. Plus, baking with sourdough discard means you’re reducing waste while creating something absolutely delicious!

What Makes These Sourdough Pumpkin Muffins Special

These aren’t your ordinary pumpkin muffins. The addition of sourdough discard gives them a unique depth of flavor that regular pumpkin muffins just can’t match. The tangy notes from the sourdough starter complement the warm spices beautifully, while the crumble topping adds a delightful crunch that contrasts with the soft, tender crumb inside.

The secret to getting those tall, bakery-style muffin tops is starting them at a high temperature (425°F) for the first 5 minutes, then lowering the heat to finish baking. This technique creates a beautiful dome and a slightly crispy top while keeping the inside perfectly moist.

Ingredient Notes and Tips for Perfect Pumpkin Muffins

Ingredients for sourdough pumpkin muffins including flour, pumpkin puree, sourdough discard, eggs, and spices on a counter - Hostess At Heart

For the Muffins:

All-purpose flour – This creates the perfect texture. Make sure to measure correctly by spooning flour into your measuring cup and leveling it off.
Pumpkin puree – Use plain pumpkin puree, NOT pumpkin pie filling. The pie filling has added sugars and spices that will throw off the recipe.
Sourdough discard – This is unfed starter from your jar. If you want even more rise, you can use an active sourdough starter instead.
Pumpkin pie spice – You can buy this pre-made or make your own by mixing cinnamon, ginger, nutmeg, and cloves like we do.
Oil – Vegetable, canola, or melted coconut oil all work great. Oil keeps these muffins extra moist.
Both white and brown sugar – The brown sugar adds moisture and a deeper flavor.
Eggs – Use room temperature eggs for better mixing.
Milk – Any milk works, including dairy-free options like almond or oat milk.

Crumble topping ingredients including brown sugar, butter, cinnamon, white sugar, and flour - Hostess At Heart

For the Crumble Topping:

Melted butter – This binds the crumble together. You can use salted, unsalted butter, or dairy-free butter if needed.
Flour and sugars – These create that perfect crumbly texture everyone loves.

How to Make Sourdough Pumpkin Muffins

Making these sourdough discard pumpkin muffins is super easy, even if you’re new to baking! Here’s how to do it:

Prep Your Pan Preheat your oven to 425°F and line your muffin pan with paper liners. This recipe makes 24 muffins, so you’ll need two standard 12-cup muffin pans.

Combined together flour, pumpkin spice, baking powder, and baking soda in a large mixing bowl - Hostess At Heart

Mix the Dry Ingredients in a large mixing bowl, whisk together your flour, pumpkin spice, baking powder, baking soda, and salt. Set this aside while you work on the wet ingredients.

Add eggs
Add Discard
Add pumpkin

Combine the Wet Ingredients. In another bowl, mix the oil with both sugars until well combined. Add your eggs one at a time, mixing well after each one. Then stir in the sourdough discard, pumpkin puree, and vanilla until you have a smooth mixture.

Fold in dry ingredients
Mix until smooth

Bring It All Together: Add your flour mixture to the wet ingredients, alternating with the milk. Mix just until everything is combined – don’t overmix or your muffins will be tough!

Mixing melted butter with flour, brown sugar, and pumpkin spice to make crumble topping - Hostess At Heart

Make the Crumble. In a small bowl, mix together the flour, sugars, and pumpkin spice for the topping. Pour in the melted butter and stir until it looks like coarse crumbs.

Fill and Top Use a large cookie scoop (about 3 tablespoons) to fill your muffin cups. Top each one with 1-2 tablespoons of the crumble mixture.

Bake to Perfection Bake at 425°F for 5 minutes, then reduce the temperature to 350°F and bake for another 20-22 minutes or until a toothpick inserted in the center comes out clean.

Cool. Let the muffins cool in the pan for 2-3 minutes, then transfer them to a cooling rack. This prevents soggy bottoms!

Overhead view of golden brown baked sourdough discard pumpkin muffins with crunchy brown sugar crumble topping in a muffin tin - Hostess At Heart

Delicious Variations to Try

Once you’ve mastered the basic recipe, try these fun twists on your pumpkin sourdough muffins:

Chocolate Chip Version – Fold in ½ to ¾ cup of chocolate chips to the batter for a sweeter treat. The chocolate pairs wonderfully with pumpkin!

Nutty Pumpkin Muffins – Add ½ cup of chopped pecans or walnuts to the batter for extra crunch and nutty flavor.

Cream Cheese Swirl – Mix 4 oz softened cream cheese with 2 tablespoons sugar and swirl it into the batter before baking.

Maple Glaze – Drizzle cooled muffins with a simple glaze made from powdered sugar and maple syrup.

Streusel Instead of Crumble – Make the topping chunkier by using cold butter instead of melted for bigger crumble pieces.

Single sourdough pumpkin muffin with the liner pulled down showing a moist tender interior and a crunchy crumble top - Hostess At Heart

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How to Store Your Pumpkin Muffins

These sourdough pumpkin muffins stay fresh and delicious when stored properly:

Room Temperature: Keep muffins in an airtight container for up to 3 days. They’ll stay nice and moist!

Refrigerator: Store in an airtight container in the fridge for up to 5 days. This is great if your kitchen is warm.

Freezer: These muffins freeze beautifully! Wrap each muffin individually in plastic wrap, then place them all in a freezer bag. They’ll keep for up to 3 months. To enjoy, thaw at room temperature for an hour or microwave for 20-30 seconds.

Muffin cut apart a warm sourdough pumpkin muffin showing the steamy moist interior - Hostess At Heart

Frequently Asked Questions

Can I use active sourdough starter instead of discard? Yes! An active, bubbly starter will work great and will actually give your muffins a little extra lift. The flavor will be slightly less tangy than using discard, but they’ll still turn out delicious.

Can I freeze the batter, or just the baked muffins? Bake first, then freeze — sourdough batter doesn’t freeze well because the leavening loses its power. Baked and cooled muffins freeze beautifully for up to 3 months.

Why did my muffins turn out dense or gummy? This almost always comes down to overmixing. Once you add the flour mixture, stir juuust until you don’t see dry streaks anymore. A few lumps are totally fine!

Can I make these ahead of time? Absolutely. Bake them the night before a busy morning, or double the batch and freeze half for later. They reheat well in the microwave for 20-30 seconds. Can I use fresh pumpkin puree instead of canned? Yes, just make sure it’s well-drained first. Fresh pumpkin puree holds more water than canned, and extra moisture can make your muffins gummy instead of tender.

Angled overhead view of sourdough discard pumpkin muffins with crunchy brown sugar crumble topping - Hostess At Heart

Ready to Bake?

These sourdough pumpkin muffins are calling your name! They’re the perfect way to use your sourdough discard while creating something your whole family will love. The combination of warm spices, tender crumb, and crunchy crumble topping makes these muffins absolutely irresistible.

I hope you enjoyed this delicious recipe as much as we do. Drop me a comment below, and don’t forget to give it a star rating. ⭐⭐⭐⭐⭐. Your comments and ratings help others decide if this recipe is for them too.

Sourdough Pumpkin Muffins Recipe

Author: Julie Menghini

Sourdough pumpkin muffins with crumble topping use your discard starter for moist, flavorful fall treats. Easy recipe makes 24 bakery-style muffins!

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Prep Time 10

Cook Time 25

Course Breakfast, Brunch

Cuisine American

Keyword: Muffin Recipe, Sourdough Discard, Sourdough muffin

Servings:

Equipment

Ingredients

1 ½ cups all-purpose flour
2 tsp pumpkin spice
1 tsp baking powder
1 tsp baking soda
½ tsp salt
½ cup oil
½ cup granulated sugar
½ cup packed light brown sugar
2 eggs
½ cup sourdough discard
1 cup pumpkin puree
1 tsp vanilla extract
¼ cup milk

Crumble

⅔ cup all-purpose flour
½ cup light brown sugar packed
2 tbsp granulated sugar
1 tsp pumpkin spice
¼ cup salted butter melted

Instructions

Preheat the oven to 425 °F.
Line a cupcake pan with liners, set aside.
In a large mixing bowl, add the flour, pumpkin spice, baking powder, baking soda, and salt. Whisk together. Set aside.
In a separate bowl, add the oil, granulated sugar, and brown sugar. Mix until all ingredients are combined.
Add the eggs, one at a time, mixing well in between each addition. I use a Danish dough whisk, but a hand mixer can also be used.
Add the sourdough discard. Mix well.
Add the pumpkin purée and vanilla and mix until you have a smooth, even batter.
Add the flour mixture, alternating with milk. Mix until all ingredients are just combined. Don’t overmix.
Using a large cookie scoop (3 tablespoons), scoop the batter into the prepared cupcake pan. Set aside.
Make the crumble. In a mixing bowl, whisk together the flour, sugars, and pumpkin spice.
Add the melted butter and mix until the mixture resembles coarse crumbs.
Use 1-2 tablespoons of the crumble to cover each pumpkin muffin.
Bake in the preheated oven for 5 minutes, then reduce the oven temperature to 350 °F for 20-22 minutes.
Cool in the pan for 2-3 minutes, then transfer to a cooling rack.

Notes

Make sure to use pumpkin puree, not pumpkin pie filling.

For this recipe, I used sourdough discard, which gives a slightly more tangy flavor. You can also use a fed sourdough starter; the muffin will have more of a lift.

I like baking my muffins at 425 degrees F for 5 minutes, then reduce to 350 degrees F to finish the baking time. This will lead to a taller muffin, crispy top, and perfectly moist inside crumb.

Storage: Store in an airtight container at room temperature for 3 days or in the fridge up to 5 days.

You can make the muffins dairy-free by using alternative milk and butter for the crumble. Flavors may vary.

Recipe variations:
Add chocolate chips to the batter (½ to ¾ cups)
Chopped nuts (pecans, walnuts,…)

Nutrition

Calories: 170kcalCarbohydrates: 25gProtein: 2gFat: 7gSaturated Fat: 2gPolyunsaturated Fat: 2gMonounsaturated Fat: 4gTrans Fat: 0.1gCholesterol: 19mgSodium: 119mgPotassium: 74mgFiber: 1gSugar: 15gVitamin A: 1672IUVitamin C: 0.5mgCalcium: 27mgIron: 1mg

Nutritional Disclaimer

This recipe was calculated using the exact brands and measurements I used to make this recipe. If you are following a strict diet please note changing anything will cause the nutritional info to change. My calculations are intended as a guide only.

Tried this recipe?Let me know how it was!

If you enjoyed these pumpkin sourdough muffins, try these other sourdough discard recipes: