These whole wheat zucchini muffins are moist and deliciously spiced with cinnamon. They are a great way to use up zucchini from your garden and to eat more whole grains.

We find ourselves making these zucchini muffins and other zucchini baked goods like our zucchini cake a lot in the summer during zucchini season. If you’ve ever grown a zucchini then you’ll know what we’re talking about.
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Whether you grow it yourself or get it from a neighbor you’re likely to end up with at least a couple huge zucchini during the summer that are too big to eat. But they are just fine to use in baked goods like zucchini muffins.
We have a lot of whole wheat muffins on this site, all made with wholesome ingredients. From carrot muffins, peach muffins, and healthy blueberry muffins to chocolate muffins.
What's Cool About This Recipe
- Whole grain: These zucchini muffins are made with 100% whole grain flour so you get that extra dose of nutrients.
- Easy to make: They are easy to make and they freeze great.
Ingredients and Substitutions
- Flour: Fresh milled flour will give you the best results, but high quality store bought flour will work too. Flours that work are:
- Whole white wheat flour (hard white wheat)
- Whole wheat pastry flour (soft white wheat)
- Cinnamon: This adds flavor to the muffins.
- Baking Soda
- Baking Powder
- Salt
- Sugar: We like using organic cane sugar like this one from Florida Crystals
- Brown sugar: We like Florida Crystals brown sugar. If you don’t have brown sugar you can use all regular sugar (as mentioned above) with a touch (½-1 teaspoon) of molasses.
- Oil: Avocado oil or olive oil are our go to but any neutral flavored oil should work.
- Egg
- Vanilla extract
- Zucchini: We have not tried this with any other squash besides zucchini.
See recipe card for quantities.
Equipment
- Mixing bowl
- Muffin tin
- Whisk
- Box grater
Variations
- Add ½ cup chocolate chips or chopped nuts
Instruction Photos
Shred the zucchini on the fine side of a box grater.
Stir the dry ingredients together in a small mixing bowl.
In a separate medium mixing bowl stir together the wet ingredients, then fold in the shredded zucchini.
Add the dry ingredients into the wet ingredients and stir until combined.
Divide the muffin batter between 6 greased standard size muffin cups.
Bake at 400° F for 15-18 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Remove the muffins from the pan and cool on a wire rack.
Serving Suggestions
Muffins are great eaten on their own for a healthy snack or quick breakfast. Here are a few ideas if you want to spice them up a bit.
- Serve warm muffins spread with salted butter
- Add a dollop of whipped cream
- Frost with cream cheese frosting for a sweet treat
- Eat with hot cereal
- Pair them with a cup of coffee or tea
Storage
Store the cooled muffins in an airtight container for 2-3 days.
Tip: Place a paper towel in the container with the muffins to soak up excess moisture and keep the muffins from going sticky.
How to Freeze
Wrap individual muffins (make sure they are cooled completely) in a few layers of plastic wrap and place in a resealable bag or container. Freeze for up to 3 months. Thaw at room temperature or in the refrigerator.
Tips From Our Kitchen
If you can get your hands on fresh milled flour we highly recommend it, it makes the most delicious, moist muffins.
If you want 12 muffins then make a double batch.
FAQ
There is no need to peel the zucchini unless there are blemishes on the skin that you want removed. In that case just peel off the spots with the blemishes.
Most of the time no, but if you’re using a giant zucchini that you let overgrow in your garden you may want to remove the seeds if they are very large. Just cut the zucchini in half lengthwise and scrape them out with a spoon.
Related Recipes
📖 Recipe
Whole Wheat Zucchini Muffins
Equipment
Ingredients
- 1 cup (128 grams) Whole white wheat flour or whole wheat pastry flour
- ¼ teaspoon Baking Soda
- ¼ teaspoon Salt
- ⅛ teaspoon Baking powder
- 1 teaspoon Cinnamon
- ¼ cup + 2 tablespoons Avocado oil or oil of choice
- ¼ cup (52 grams) Packed brown sugar
- ¼ cup (52 grams) Cane sugar
- 1 large Egg
- ½ teaspoon Vanilla extract
- 1 cup Packed shredded zucchini 1 medium zucchini
Instructions
- Preheat oven to 400° F
- In a small mixing bowl stir the dry ingredients together.1 cup (128 grams) Whole white wheat flour, ¼ teaspoon Baking Soda, ¼ teaspoon Salt, ⅛ teaspoon Baking powder, 1 teaspoon Cinnamon
- In a large mixing bowl whisk together the oil, sugars, eggs and vanilla extract. Then using a rubber spatula fold the zucchini in.¼ cup + 2 tablespoons Avocado oil, ¼ cup (52 grams) Packed brown sugar, ¼ cup (52 grams) Cane sugar, 1 large Egg, ½ teaspoon Vanilla extract, 1 cup Packed shredded zucchini
- Add the dry ingredients to the wet ingredients and fold/gently stir until combined and no pockets of flour remain.
- Divide the batter between 6 greased standard size muffin cups (they will be quite full). Bake for 15-20 minutes or until a toothpick inserted in the center of a muffin comes out clean.
- Allow to cool in the pan for a couple minutes. Then remove them from the pan and place on a wire rack to cool.
Notes
Nutrition
We calculate these nutritional facts using an estimate and they can vary drastically between ingredients used and measuring technique. So, they are not intended for medical use.
Did you make this recipe? We would love to hear from you!