Last Updated on October 6, 2025 by Carrie Korem, FNTP
These pumpkin zucchini sourdough muffins are soft, lightly sweet, and packed with cozy fall flavors. Fermenting the batter overnight breaks down gluten, phytic acid, and sugars, making these muffins gentler on the digestive system while still tasting amazing.
If you’re looking for a fun way to use your sourdough starter during baking season, this is the perfect recipe to try.
How to Make Sourdough Muffins
This recipe is made in two parts: an overnight ferment, and then mixing and baking the next day.
Step 1: Overnight Ferment
- In a large mixing bowl, stir together flour, sourdough starter, sugar, pumpkin, melted butter, and milk.
- Cover tightly and refrigerate for 24 hours. This long ferment is what gives the muffins their tang and health benefits.
Step 2: Mix the Wet Ingredients
- The next day, set the dough out on the counter so it can come to room temperature. This takes about 4 hours.
- Preheat the oven to 350ºF and line your muffin tin with unbleached parchment liners.
- In a medium bowl, whisk together shredded zucchini, vanilla, eggs, and yogurt. Stir in the cinnamon, nutmeg, baking soda, and salt.
Step 3: Combine and Bake
- Add the wet ingredients to the fermented flour mixture and mix gently on low speed. Don’t overmix — this can make the muffins tough.
- Spoon the batter into the muffin tins, filling about ¾ full.
- Bake for 25–28 minutes, until the tops are golden brown.
- Cool and enjoy!
Tip: The batter might seem a little dry when you’re scooping it, but the zucchini will release moisture as the muffins bake, making them soft and tender.
How Long Do Sourdough Muffins Last?
Sourdough muffins stay fresh at room temperature for about 2 days. If you have any left after that, transfer them to the refrigerator for up to 4 more days. You can also freeze them for longer storage.
How to Store Sourdough Muffins
The best way to store sourdough muffins is on a cake stand with a top or in a glass Tupperware with a tight-fitting lid. If freezing, place them in a single layer in an airtight bag or container. Reheat them in the oven to bring back their fresh-baked texture.
Are Sourdough Muffins Healthier?
Yes, sourdough muffins are easier to digest and can more nutrients than muffins made with just wheat flour. Slow fermentation breaks down gluten and phytic acid and begins to predigest sugars. This process not only improves digestibility but also increases the availability of nutrients and can even add a bit of beneficial bacteria.
While this recipe still contains some sugar and gluten, the fermentation process transforms it into a more nourishing option.
If you’re curious to learn more about the science of sourdough, check out this podcast episode that dives deeper into fermentation and gut health.
Sourdough Muffin Recipe
Ingredients
Overnight Ferment
- 250g organic all-purpose flour
- 100g bubbly sourdough starter
- 188g organic brown cane sugar
- 125g pureed organic pumpkin
- 133g melted unsalted butter, cooled
- 60g whole milk, room temperature
Next Day
- 200g shredded zucchini
- 11g vanilla extract
- 2 large eggs, room temperature
- 160g plain whole yogurt, room temperature
- 3g cinnamon
- Dash of nutmeg
- 7g baking soda
- 1g Celtic sea salt
Instructions
- Overnight Ferment: Stir together all overnight ingredients in a large bowl. Cover and refrigerate for 24 hours.
- Warm Up: The next day, let the mixture sit at room temperature for 4 hours. Preheat oven to 350ºF. Line muffin tins with parchment liners.
- Mix: In a separate bowl, combine zucchini, vanilla, eggs, yogurt, cinnamon, nutmeg, baking soda, and salt. Mix into the flour mixture gently.
- Bake: Spoon into muffin tins, filling ¾ full. Bake 25–28 minutes, until golden. Cool before storing.
Tips for Baking the Best Sourdough Muffins
- Always use room temperature ingredients to keep the batter smooth.
- A standing mixer makes mixing easier, but a hand mixer works too.
- Don’t skip the overnight ferment—it’s what sets these muffins apart!
Here are some other fermented sourdough recipes that you might enjoy!
Fermented Sourdough Cinnamon Rolls
Fermented Sourdough Bread
Overnight Fermented Sourdough Pancakes
Fermented Sourdough Chocolate Chip Cookies
Pumpkin Zucchini Sourdough Muffins
The next day:
- 200g shredded zucchini
- 11g vanilla extract
- 2 large eggs, room temperature
- 160g whole, plain yogurt, room temperature
- 3g cinnamon
- A dash of nutmeg
- 7g baking soda
- 1g celtic sea salt
Instructions
Place the flour, starter, sugar, pumpkin, butter and milk in a large mixing bowl and stir until combined. Cover tightly and place in the refrigerator for 24 hours.
The following day, remove the dough mixture and let sit out on the counter for about 4 hours so it reaches room temperature.
Preheat the oven to 350ºF and adjust the rack to the middle position. Line a muffin tin with unbleached parchment liners.
Transfer the flour mixture to the bowl of a standing mixer. You can also use hand-held beaters.
In a medium-size bowl, combine the zucchini, vanilla, eggs and yogurt. Whisk to combine. Stir in the cinnamon, nutmeg, baking soda and salt and then immediately, add the zucchini mixture into the flour mixture and mix on low using the beater. Mix until just combined and do not over mix (this will make the dough tough).
Spoon equal portions of dough into each muffin cup, filling the cups about 3/4 full. Bake for 25-28 minutes, until just turning golden brown. Remove from oven and cool. Repeat with remaining batter.
Leftovers can be frozen and then reheated in the oven, or store in the fridge for 3-4 days and reheat in the oven before serving.
