These moist and flavorful Sourdough Pumpkin Muffins make morning routines easy, cozy, and delicious.

What makes these sourdough pumpkin muffins so special? They’ve got the classic cinnamon, ginger, and cloves we love, but I’ve added a tiny kick of cayenne pepper. Don’t worry, it’s not enough to make them spicy—it’s just enough to create a cozy warmth that perfectly complements the rich pumpkin flavor. It’s the secret ingredient that will have everyone guessing what makes these muffins so warm and good.
But the best part is how easy they are. Made with sourdough starter, these muffins come together quickly, making them the perfect make-ahead breakfast or after school snack. Wake up to one of these beauties or grab one on your way out the door… They’re soft, perfectly moist, and packed with flavor… And they stay fresh for days! So bake a big batch and get ready to fall in love with my new favorite autumn staple.
Pumpkin season is my absolute favorite, and I’m a firm believer that it’s a flavor that can do it all! If you’re as obsessed as I am, you’ll want to check out some of my other favorite pumpkin recipes. From classic bakes like my gooey Pumpkin Cinnamon Rolls and rich Pumpkin Coffee Cake to a perfectly flaky Pumpkin Pie, I’ve got you covered. And don’t stop there—pumpkin is amazing in savory dishes too, like my cozy Pumpkin Curry and hearty Pumpkin Chili. There’s no end to the fall goodness!

Baking the Best Sourdough Pumpkin Muffins
Let’s get into the nitty-gritty to make sure your muffins come out absolutely perfect. You’ll thank me later for these tips!
Sourdough Starter is Your Secret Weapon: This recipe is seriously the best way to use up your sourdough discard. We aren’t looking for a bubbly, active starter here. The baking soda in the recipe is what gives these muffins their amazing lift and texture, while the starter just adds that incredible depth of flavor.
The Cayenne Kick: I know what you’re thinking—cayenne pepper in a muffin?! Trust me on this one. It’s not about making them spicy; it’s about adding a subtle, cozy warmth that just feels like fall. It’s that secret ingredient that will have everyone trying to figure out why your muffins are so good!
Don’t Overmix!: This is the most important rule for baking muffins. When you add the wet ingredients to the dry, just fold everything together until it’s barely combined. A few lumps of flour are totally fine! Overmixing is a surefire way to get tougher, denser muffins 😉
Storing and Freezing for Later
One of my favorite things about these muffins is how well they keep. Make a big batch on a Sunday, and you’ve got delicious breakfasts ready to go for the whole week!
For the short-term: Just store your cooled muffins in an airtight container on the counter. They’ll stay perfectly moist and delicious for about 3 to 4 days. Wait till they’re completely cooled before putting them in the container so they don’t sweat;)
For the long-term: These muffins freeze beautifully! Once they’re completely cool, pop them into a freezer-safe bag or container. They’ll stay fresh and ready to eat for up to 3 months. To enjoy one, just pull it out and let it thaw on the counter, or give it a quick zap in the microwave for a warm, gooey treat.
Mix-and-Match Your Ingredients
Don’t have every single ingredient? Or maybe you’re just feeling a little creative? No problem! Here are a few ways you can switch things up to make this recipe your own:
Spice It Up: If you’re missing a few spices, you can totally substitute the cinnamon, ginger, and cloves with about 2 teaspoons of pumpkin pie spice. You could also use nutmeg or allspice. Easy peasy.
Top it Off: If you don’t have time for the streusel, a simple sprinkle of cinnamon sugar on top before baking is a delicious and easy alternative. You could also toss a handful of chocolate chips or chopped pecans into the batter for a little something extra special.
I want to know what YOU think… Please review the recipe card!

Moist Sourdough Pumpkin Muffins with Streusel Topping
Ingredients
Dry Ingredients
- 2 3/4 cups all-purpose flour 360 g of whole grain flour
- 1 1/2 cups sugar granulated
- 1 1/2 tsp baking soda
- 1 tsp salt
- 2 tsp cinnamon powder
- 1/2 tsp ground ginger
- 1/2 tsp ground cloves
- 1/4 tsp cayenne pepper
Wet Ingredients
- 1 cup sourdough starter discard
- 15 ounces pumpkin puree without sugar and spices
- 4 large eggs
- 1 cup olive oil
Streusel Topping
- 1/2 cup flour all purpose or whole grain
- 1/2 cup brown sugar
- 1 tsp cinnamon
- 1/3 cup cold butter cut into small pieces
Instructions
- Preheat your oven to 350°F (175°C) and line a 12-cup muffin tin with paper liners.
- In a large bowl, whisk together all the dry ingredients for the muffins: flour, sugar, baking soda, salt, cinnamon, ginger, cloves, and cayenne pepper.
- In a separate medium bowl, whisk together the wet ingredients: pumpkin puree, sourdough starter, eggs, and olive oil.
- Pour the wet ingredients into the dry ingredients. Use a spatula to fold the mixture together until just combined. Be careful not to overmix!
- In a small bowl, prepare the streusel topping. Combine the flour, brown sugar, and cinnamon. Cut in the cold butter using your fingers or a pastry blender until the mixture forms coarse, pea-sized crumbs.
- Divide the batter evenly among the prepared muffin cups, filling each about three-quarters full.
- Sprinkle about 1 tablespoon of streusel topping over the top of each muffin.
- Bake for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Let the muffins cool in the pan for a few minutes before transferring them to a wire rack.
Notes
Nutrition
About Juliea
Juliea Huffaker is the creator of Farmhouse Harvest, and dedicated to teaching from-scratch cooking, sourdough baking, gardening, and food preservation. With over 25 years of hands-on experience she has preserved hundreds of jars of produce, mastered the art of meats and sourdough baking, and nurtured a thriving organic garden. Her recipes and articles have been featured across the web. And she’s passionate about inspiring others to embrace a simpler, self-sufficient life style.
3 comments
Timber
Be carful with these ones I ate way to many they are so delicious!
Boden
Was super surprised at how good these are. I ate 5 in a row without even thinking about it.
Sadie
These muffins are so full of flavor and are hard to stop eating! The spices and sweetness are a perfect blend!