Light, tender, and full of cozy pumpkin spice, these Sourdough Pumpkin Muffins are an easy way to use up sourdough discard. Finish them with a silky honey cream cheese glaze for an extra special touch.

Muffins have become one of my favorite ways to use up sourdough discard, and these pumpkin sourdough muffins might just be my favorite fall version. Pumpkin purée, brown sugar, and sourdough discard come together to make a muffin that’s delightfully light, soft, and moist, with all the classic warm spices to make them super flavorful.
They’re delicious as is, but the cream cheese glaze takes them to another level. It’s the same glaze I use for my Fig & Brie Cinnamon Rolls, and the sweet honey flavor and tangy cream cheese make the perfect finishing touch. The muffins are quick and easy to throw together, so you can enjoy a delicious fall bake in about half an hour.
Recipe highlights
- So soft & moist thanks to pumpkin puree, oil, & sourdough discard
- Classic fall flavors with warm baking spices
- Lovely for breakfast, snacking, or even dessert
- Super easy & quick to mix by hand (ready in about 30 minutes!)
Recipe overview
⏱️ Prep: 10 mins • Bake: ~20 mins • Total: ~30 mins
🍴 Yield: 12 muffins
💪 Skill level: Beginner
😋 Flavor notes: Pumpkin, cinnamon, ginger, honey, cream cheese, sourdough tang. Pairs well with: Breakfast & brunch spreads, soft butter, whipped cream, coffee.
👉 Love sourdough muffins? Check out Raspberry Lemon Sourdough Muffins, Sourdough Banana Chocolate Chip Muffins, and Sourdough Corn Muffins.
How to make pumpkin sourdough muffins
Find the full ingredients list and detailed recipe instructions in the recipe card at the bottom of this post. Here’s a quick step-by-step overview of how to make this recipe:
- Prep: Preheat the oven to 425° F. Line a muffin pan with paper liners.
- Whisk together wet ingredients: Mix pumpkin purée with brown sugar, oil, eggs, sourdough discard, and vanilla.
- Whisk dry ingredients: In a medium bowl, whisk together flour, baking powder, baking soda, spices, and salt.
- Fold everything together gently: Pour dry ingredients into wet ingredients, then fold it all together gently with a spatula until mostly combined – don’t overmix.
- Bake: Scoop batter into prepared muffin pan, filling tins all the way to the top. Bake for 5 minutes, then turn the oven down to 350° F and bake an additional 13-17 minutes, or until the tops are lightly golden and spring back when touched. Cool completely.
- Make glaze: While muffins are cooling, beat cream cheese, butter, honey, and vanilla together until creamy and smooth. Drizzle onto cooled muffins and enjoy!




Pro baker’s tips for perfect pumpkin muffins
Mix gently! To achieve super tender and light sourdough pumpkin muffins, avoid over-mixing or vigorously beating your batter. Fold the dry and wet ingredients together gently with a spatula, and stop mixing when it’s almost combined. A slightly lumpy batter is just fine here.
Use an unfed sourdough starter. The sourdough starter in this recipe is used for flavor and its ability to make baked goods super tender. We’re not using it to make the muffins rise in this case (that’s what the baking powder & soda are for).
Take them out of the oven as soon as they’re ready. When the tops are golden and spring back lightly when touched, they’re ready! Remember that muffins will continue to bake a little bit after you remove them from the oven. Over-baked muffins = dry muffins.
If in doubt, use a digital thermometer. The internal temperature of muffins should be right around 200° F.

Variations
Add some texture: Feel free to fold in ½ – 1 cup chocolate chips, craisins, or chopped pecans just after mixing in the flour. Just be sure not to mix too much!
Switch up the topping. Skip the cream cheese glaze and try any of these instead:
- Brown butter glaze from my Giant Apple Cinnamon Roll
- Salted maple glaze from this Pumpkin Cinnamon Focaccia
- Vanilla cinnamon glaze from my Apple Coffee Cake
- Sprinkle the tops of the muffins with coarse sugar before baking for a crunchy sugar topping (like I did for these Sourdough Huckleberry Muffins)
- Brush the warm muffins with melted butter after baking and roll in a cinnamon sugar mixture (try the spiced sugar I used to top my Cinnamon Swirl Banana Bread)
How to store
Keep your sourdough discard pumpkin muffins in an airtight container at room temperature for up to 3 days. You can also store them in the refrigerator, but they’ll dry out a bit more.
What to bake next: You might want to try this Sourdough Pumpkin Chocolate Chip Bread, or cruise through my collection of sourdough discard recipes for more inspiration!

If you make these Sourdough Pumpkin Muffins, please leave a comment & star rating. It helps other bakers and means a whole lot to me!

Sourdough Pumpkin Muffins
Equipment
- Muffin tin & paper liners
Ingredients
Sourdough pumpkin muffins
- 1 15-oz can pumpkin purée (or 1 ½ cups homemade pumpkin purée)
- 1 cup brown sugar
- ½ cup neutral vegetable oil, I like avocado oil
- 2 eggs
- ½ cup sourdough discard
- 1 teaspoon vanilla
- 2 cups (240 grams) all purpose flour
- 2 teaspoons baking powder
- ½ teaspoon baking soda
- ¾ teaspoon cinnamon
- ½ teaspoon ground ginger
- ½ teaspoon ground nutmeg
- ⅛ teaspoon ground cloves
- 1 teaspoon salt
Honey cream cheese glaze
- 4 ounces cream cheese, soft, room temperature
- 2 ounces (4 Tbsp) unsalted butter, soft, room temperature
- ¼ cup honey
- 1 ½ teaspoons vanilla
Instructions
- Prep: Preheat the oven to 425° F. Line a muffin pan with paper liners.
- Whisk together wet ingredients: In a large bowl, mix 15 oz/ 1 ½ cups pumpkin purée with 1 cup brown sugar, ½ cup oil, 2 eggs, ½ cup sourdough discard, and 1 tsp vanilla until thoroughly combined.
- Whisk dry ingredients: In a separate bowl, whisk together 2 cups/240 grams flour, 2 tsp baking powder, ½ tsp baking soda, ¾ tsp cinnamon, ½ tsp ginger, ½ tsp nutmeg, ⅛ tsp cloves, and 1 tsp salt.
- Fold everything together gently: Pour dry ingredients into wet ingredients, then fold it all together very gently with a spatula until mostly combined. Use a light hand and avoid over-mixing. A lightly lumpy batter is fine here.
- Bake: Scoop batter into prepared muffin pan, filling tins all the way to the top. You should use all the batter for 12 muffins.Bake for 5 minutes, then turn the oven down to 350° F (leave the muffins in the whole time), and bake an additional 13-17 minutes, or until the tops are lightly golden and spring back when touched. Remove from oven and allow to cool completely.
- Make glaze: While muffins are cooling, beat 4 oz cream cheese until completely smooth and free of lumps. Add 2 oz soft butter, beating until well mixed and smooth. Then add ¼ cup honey and 1 ½ tsp vanilla, blending until creamy and silky. Spoon or drizzle glaze onto cooled muffins and enjoy!
Notes
Did you try this recipe?
Be sure to leave a comment below!


