Got lots of garden zucchini? Turn it into the most wholesome and delicious sourdough zucchini muffins!

Right now, I have three massive, 1.5-foot-long zucchini sitting on my kitchen counter, and at least three more waiting out in the garden! I only plant a single zucchini plant each year—because anything more and I’d be completely overwhelmed—and my 7-year-old son loves to go out and harvest them for me. He carries each giant squash inside like a prized trophy, so proud of his catch!
Recipes like these sourdough zucchini muffins are a total lifesaver for using up that summer abundance. Even better? They freeze beautifully, making them ideal for quick, homemade breakfasts on busy school mornings.
These sourdough zucchini muffins make the best breakfast… They’re packed with zucchini, the benefits of sourdough, and are perfectly moist! Just like my Fluffy Sourdough Pancakes and Crispy Sourdough Waffles, to the comforting Sausage Gravy and Biscuits… I’ve got your mornings covered!

Long Fermentation (Why You May Want to Try It!)
Long fermentation might sound fancy, it’s actually very simple, and optional but recommended for these muffins, if you have the time.
Why bother letting your batter ferment for 8-12 hours (overnight)? It gives your sourdough starter more time to work its magic, truly transforming your muffins! Here’s the scoop on the benefits:
- Deeper Flavor: Your muffins get an even richer, more complex taste as the sourdough develops incredible flavor.
- Lovely Texture: While baking soda and powder do the heavy lifting for rise, fermentation really contributes to a nice tender crumb. 😉

How it Works (and Why Timing Matters!)
If you long ferment, simply mix your wet and dry ingredients (holding back the baking soda and baking powder!), fold in the zucchini, cover, and let it sit. You might notice slight bubbling—that’s your sourdough doing its thing!
Do NOT add the baking soda and baking powder until after the fermentation. The baking soda needs acid to react and create lift. During the long ferment, your sourdough produces more of that beneficial acid. Adding the baking soda, and baking powder right before baking gives it plenty to react with, so your muffins have the best rise and texture. 😉

Key Ingredients
Let’s chat about the stars of the show for these delicious sourdough zucchini muffins! While every ingredient plays a role, these are the ones that really make the magic happen. Don’t worry, we’ve got some friendly tips and easy swaps for you too!
Active Sourdough Starter (or Discard): This is truly the heart of our recipe! “Active” means your starter is bubbly, fed, and ready to go… Ideally, it should have been fed 4–12 hours before you plan to bake. A lively starter is key for flavor and for helping with that tender crumb, especially if you opt for long fermentation!
- Baking with Discard? Since baking powder and baking soda provide the main rise in this recipe, unfed sourdough discard can also be used directly in the quick-bake (non-fermented) version without sacrificing any rise!
Zucchini: Of course! You’ll need about 1-2 medium zucchini to get your 2 cups.

Flour (Whole Wheat, Einkorn, OR Unbleached All-Purpose):
Whole Wheat or Einkorn: These types of flour will give your sourdough zucchini muffins a more rustic, nutty flavor and a denser, heartier texture. Plus, they add extra fiber – bonus!
Unbleached All-Purpose Flour: If you prefer a lighter, softer muffin, or if that’s just what you have in your pantry, all-purpose flour is a perfectly fantastic choice. It’s reliable and will give you a classic muffin texture. Feel free to mix and match too!

Baking Soda & Baking Powder: These are your leavening agents, they that gives your sourdough zucchini muffins that wonderful rise! They work together, especially with the acidity from the sourdough. Remember our note about when to add them – it’s important!
*Improtant – Do NOT add baking soda/powder before long fermenting!
Oil (Olive Oil or Avocado Oil): We’re using oil here for a super moist and tender muffin. Both olive and avocado oil are great choices because they have a mild flavor that won’t overpower the zucchini and cinnamon, plus they add to that lovely soft texture. If you only have another neutral-flavored oil like melted coconut oil (liquid form), that would work in a pinch, but I prefer olive or avocado.
Eggs: These are super improtant… They bind everything together, add moisture, and add richness and structure of your muffins. They’re pretty essential!


How to Prep Zucchini So Muffins Aren’t Soggy
Zucchini is full of natural moisture, which is fantastic for creating a tender muffin—until excess water turns the crumb gummy or heavy. How you handle your zucchini makes all the difference in getting that light, bakery-style rise!
Squeezing vs. Not Squeezing
In this recipe, we rely on a little bit of natural zucchini moisture to balance the flour and flax seed, but you don’t want liquid pooling at the bottom of your bowl!
- Standard Shred (Recommended): Use the medium or large holes on a box grater. Gently press the shredded zucchini between a few sheets of paper towels or a clean kitchen towel to remove surface wetness. You do not need to wring it bone-dry, just remove the dripping excess water.
- If Using Large/Late-Season Zucchini: Summer garden giants tend to carry far more water and larger seeds. Scoop out the watery seed center before grating, and give the shredded flesh a slightly firmer squeeze.
💡 Quick Tip: Shred your zucchini on a box grater, toss it in a colander with a tiny pinch of salt, and let it sit for 10 minutes while you measure your other ingredients. The salt draws out extra moisture naturally! Wrap it in a tea towel and give it a gentle pat before folding it into your batter.

Troubleshooting & FAQ’s
Why did my crumble topping sink? If your crumble sunk intot he batter it was one of 2 problesm… Either the butter was too warm, or the streusel topping was sprinkled too heavily in the center rather than evenly over the top.
Can I freeze these? Yes, just wrap them individually in plastic wrap, then store them in a freezer bag for up to 3 months… They make a great grab and go breakfast!
Can I substitute frozen zucchini? Yes you can grate and freeze your zucchini, then thaw it completely, and drain the liquids off before measuring it into your muffin batter.
Did you make these sourdough zucchini muffins? I wanna know what YOU think… Please leave a review!

Sourdough Zucchini Muffins with Crumble Topping
Ingredients
- 2 cups flour whole wheat, einkorn, OR unbleached all-purpose flour
- ¾ cup granulated sugar pure cane sugar recommended
- ¾ cup ground flax seed
- 1 teaspoon salt
- 1 teaspoon baking soda See Note on Fermentation below
- 1 teaspoon baking powder
- 2 cups grated zucchini
- ½ cup active sourdough starter
- 1 teaspoon vanilla extract
- 1 teaspoon cinnamon powder
- 2 large eggs
- ⅔ cup olive oil or avocado oil
For the Crumble Topping:
- ½ cup granulated sugar
- ⅓ cup flour einkorn or all-purpose
- ¼ cup cold butter cubed
- 1 ½ teaspoons ground cinnamon
Instructions
Combine Dry Ingredients (Except Baking Soda and powder, if Fermenting):
- In a large bowl, whisk together the 2 cups flour, ¾ cup granulated sugar, ground flax seed, salt, 1 teaspoon baking powder, 1 teaspoon baking soda, and 1 teaspoon cinnamon powder. If you plan to long ferment, do NOT add the baking soda and powder yet.
Mix Wet Ingredients:
- In a separate medium bowl, whisk together the active sourdough starter, vanilla extract, eggs, and ⅔ cup olive oil until well combined.
Combine Wet and Dry:
- Pour the wet ingredients into the dry ingredients and mix until just combined. Be careful not to overmix; a few lumps are fine.
Add Zucchini:
- Gently fold in the grated zucchini.
- Optional Long Fermentation (for enhanced flavor and digestibility):
- If you are long fermenting: Cover the bowl with plastic wrap or a clean kitchen towel and let it sit at room temperature for 8-12 hours, or overnight.
- If you are NOT long fermenting: Proceed to the next step.
Incorporate Baking Soda (Crucial Step):
- If you long fermented: After the fermentation period, stir in the 1 teaspoon of baking soda and 1 teaspoon baking powder and stir thoroughly. This will react with the acids in the sourdough to create a lighter texture.
- If you did NOT long ferment: Add the 1 teaspoon of baking soda and baking powder along with the other dry ingredients in step 1.
Prepare the Crumble Topping:
- In a small bowl, combine the ½ cup granulated sugar, ⅓ cup flour, and 1 ½ teaspoons ground cinnamon. Add the cold, cubed butter. Use your fingertips or a pastry blender to cut the butter into the dry ingredients until the mixture resembles coarse crumbs.
Bake the Muffins:
- Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease it well.
- Divide the muffin batter evenly among the 12 muffin cups.
- Generously sprinkle the crumble topping over each muffin.
- Bake for 20-25 minutes, or until a wooden skewer or toothpick inserted into the center of a muffin comes out with only a few moist crumbs attached.
- Let the muffins cool in the muffin tin for a few minutes before transferring them to a wire rack to cool completely.
Notes
Nutrition

About Juliea
Juliea is a mother of six, a sourdough baker, and a homestead builder living in Idaho. Alongside her husband and their horse, Dude, she manages a busy farmhouse and shares her love for scratch-cooking and simple homemaking. Through her blog and YouTube channel, she helps millions of families every year master the art of the handmade home.










1 comment
Timber
Delicious moist and easy to make! Can I make it with bananas?