Healthy Whole Wheat Zucchini Muffin Recipe

These whole wheat zucchini muffins are soft, moist, and made especially for freshly milled flour. They’re a wholesome and delicious way to enjoy fresh zucchini in an easy homemade treat.

If you’ve ever struggled to grow a vegetable garden, I’d suggest that you try a zucchini plant. Zucchinis are a mild flavored vegetable that produces like gang busters. Perfect for making healthy desserts and snacks like zucchini bread, cake and muffins. How many vegetables can make a claim like that?

Today, I’m using some of my abundant zucchini harvest to add nutrition, flavor and moisture to my already delicious basic muffin recipe. I’ve made a couple of adjustments to the muffin ingredients to get everything just right, and I’m loving the results.

If you’re a fan of zucchini muffins or zucchini bread, you’ll love this recipe. Even if you’re not, I dare you to try these zucchini muffins and not fall in love with them. Made with freshly milled whole wheat flour, these muffins are incredibly healthy and taste divine!

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Fresh Milled Flour Makes the Best Muffins

If you know me, you’ll know I love freshly milled flours. I mill all of my flour from wheat berries. It’s a quick and easy process that you can read about in how to mill your own flour and the health benefits.

Fresh milled flour is the best kept secret in baking. In a nutshell, you get the best flavor and the most nutrients from your flours within the first hours and days after they are milled. Quality declines significantly after that.

You have no way of knowing how long a bag of flour has been sitting on your grocery store shelf. That’s why I use fresh milled flour for muffins and everything else. It’s top quality every time!

For tips on how to get perfect muffins every time, checkout my muffin making tips.

Whole Wheat Zucchini Muffin Ingredients

Wet Ingredients

• 1 cup plain yogurt
• 2 large eggs
• ½ cup honey
• ½ cup melted and cooled coconut oil or butter (or ¼ cup butter + ¼ cup coconut oil)
• 1 teaspoon pure vanilla extract
• 1 cup grated zucchini (about 1 medium zucchini) *

* If you don’t want to see any green flecks in your muffins, you can use a food processor to get a finer zucchini texture. I find that this method makes the finished muffin feel slightly more wet and doughy, but still super tasty. Grated zucchini is my preference for perfect texture.

Dry Ingredients

• 2 cups (260 grams) freshly milled flour 
• 1 teaspoon salt
• 1 ½ teaspoon baking powder
• ½ teaspoon baking soda
• 1 teaspoon ground cinnamon
• ¼ teaspoon nutmeg

How to Make Whole Wheat Zucchini Muffins

Preheat oven to 425°F (220°C). Grease a muffin tin and set aside.

Squeeze out any excess moisture from the shredded zucchini, and set aside.

In a large bowl, whisk together all of the wet ingredients (including the shredded zucchini) until smooth and well combined.

Add the freshly milled flour and salt to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.

After resting, sprinkle in the baking powder, baking soda, cinnamon, and nutmeg. Mix gently until everything is evenly combined, being careful not to overmix.

Working quickly, spoon the muffin batter into the prepared muffin tin, filling each cup evenly.

Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 10-12 minutes, or until the centers feel firm and the muffins are baked through.  The zucchini adds moisture, so these muffins take a little longer to cook.

Remove from the oven and let cool slightly on a wire rack — or enjoy warm right away.

*These are basic zucchini muffins, but feel free to get creative and add extras like chopped walnuts, chocolate chips, coconut shreds, cranberries, etc.

Printable Zucchini Muffins Recipe Card for

Storing Muffins

Store cooled muffins in an airtight container at room temperature for up to 2 days.

For longer storage, wrap the muffins and place in a freezer safe container or bag the same day that they’re baked. Store for up to a few weeks. Thaw at room temperature before serving.

Where to get Baking Supplies

If you need baking supplies, checkout the Bread Making Supplies page. It’s where I share information and links to all my baking favorites. Only the best products make it onto this page!

More Recipes Like This

If you’re looking for the perfect breakfast, snack or healthy dessert that even the kids will love, this is it. These whole wheat muffins are zucchini season favorite. Try it today and see what I mean!

For more muffins and freshly milled whole wheat recipes, see: