Healthy Zucchini Muffins

Name: Healthy Zucchini Muffins
Prep time: 10 min
Cook time: 20 min
Total time: 30 min
Ingredients: 2 large eggs; 1/2 cup applesauce or yogurt; 1/2 cup honey or maple syrup; 1/4 cup any mild tasting oil; 1 tsp pure vanilla extract; 1 tsp cinnamon; 1 tsp baking powder; 1/2 tsp baking soda; 1/4 tsp salt; 2 cups whole wheat or spelt flour; 2 cups shredded zucchini (not squeezed and packed); 1/2 cup walnuts (optional); Cooking spray (I use Misto)

By Olena Osipov

4.87 from 58 votes

May 15, 2025

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Healthy Zucchini Muffins are easy to make in one bowl and super delicious! They are light, fluffy and moist muffins loaded with flecks of zucchini!

We love baking muffins with zucchini like these lemon zucchini muffins, chocolate zucchini muffins and banana zucchini muffins.

Healthy zucchini muffins in paper liners stacked on top of each other, fresh zucchini.

These healthy zucchini muffins are inspired by my whole grain healthy zucchini bread and healthy zucchini banana bread. They taste amazing!

Baking healthy muffins is one of my favorite ways to make sure my kids are eating healthy. It comforts me as a mom, to know they are not eating a lot of sugar and empty calories when they grab-n-go.

Why You’ll Love This Recipe

Easy to make: In one bowl and ready in 30 minutes.
Fiber fueled: Swapping white flour for whole grains add fiber and keeps you full longer.
Lower in sugar: The only added sweetener is maple syrup.
Lower in fat: Swapping some of the oil retains moisture but lowers the fat consumption.
Veggies: A full 2 cups of zucchini in 12 muffins means you are getting an extra serving of veggies!

Ingredients for Healthy Zucchini Muffins

The best part about these zucchini muffins is that you probably have most ingredients on hand right now.

Zucchini, whole wheat flour, applesauce, maple syrup, oil, vanilla extract, eggs, cinnamon, baking powder, baking soda, salt, oil.

Zucchini: You will need 2 cups of shredded zucchini that has not been squeezed.
Eggs: Used for binding.
Applesauce: Sweetened one will yield sweeter results, I use unsweetened.
Maple syrup or honey: Both pack a sweet punch and each will result in a slightly different taste, use what you prefer.
Pure vanilla extract: Pure vs. imitation for best taste results.
Cinnamon: A lovely spice that pairs well with vanilla, and yes, even the zucchini.
Baking powder and soda: Used to create light and airy texture. Find aluminum free baking powder, if you can.
Whole wheat flour: Regular whole wheat or spelt flour is best, see Substitutions below for gluten free flour.

How to Make Healthy Zucchini Muffins

A few easy steps, one bowl and you are well on your way!

Prep: Shred zucchini using a box grater. Do not squeeze. Prep and spray muffin tin. Set aside.
Mix liquid ingredients: Add eggs, applesauce, maple syrup, oil, vanilla extract, cinnamon, baking powder, baking soda and salt to large mixing bowl. Whisk well to combine until no small lumps of baking powder and soda are left.
And in flour and zucchini: Add flour and stir until just combined. I like to leave it with a few patches of flour for about 3 minutes and stir again. Fold in shredded zucchini.
Bake the muffins: Distribute batter with regular ice cream scoop evenly between 12 openings of a muffin tin and bake for 20 minutes or until a toothpick inserted in the center comes out clean.

Baked zucchini muffins in blue muffin tin.

Cool: Let muffins cool for a few minutes then transfer to a cooling rack to cool off completely.

Tips for Best Results

Shredding zucchini: I like to use largest holes of the box grater so you can see those pretty green speckles of zucchini. You can also use smaller hole side “to hide” the veggies.
No need to peel zucchini: First, there is no need to peel the zucchini first. The skin is thin, light, and edible. You won’t taste the difference once baked and the flecks of dark green from the zucchini and skin look nice.
Do not squeeze out excess water: There are some recipes that will require you to squeeze the excess moisture out for a zucchini muffin recipe but this is not one of those times because the moisture is needed.
Large garden zucchini: While a thinner zucchini is usually preferred for baking and zucchini noodles, you could use a larger garden zucchini, but may prefer to remove the seeds as they can be bitter.
Do not overmix the batter: Be careful to stir just until your muffin batter is combined. The batter will thicken as dry ingredients absorb moisture. Over mixing will cause your healthy zucchini muffins to be dense.
Do not overbake the muffins: Remove from the oven as soon as toothpick inserted in the center comes out clean. Muffins will keep baking with residual heat.

Five healthy zucchini muffins with one unwrapped with a bite missing.

Additions and Substitutions

Yogurt: You can replace applesauce with yogurt but muffins will be less sweet. Use regular yogurt or Greek yogurt. Generally 2% fat and higher will yield better results.
Swap applesauce for mashed bananas: They will act the same way by providing moisture and replacing the oil but will give off a bit of a different taste.
Nuts or fruit: Add up to 1/2 cup of chopped walnuts, pecans, or almonds. Fresh or frozen blueberries, dried raisins, or mini chocolate chips would be great as well.
Mini muffins: Cut baking time in half, check for doneness and either remove or add 1-2 minutes extra time.
Making muffins gluten free: Use 2 3/4 cups all-purpose gluten free flour instead of whole wheat flour and add 1 teaspoon cornstarch.
Love almond flour? Try these almond flour zucchini muffins which are also naturally gluten free!
Need egg free? Readers have had success with flax eggs or chia eggs.

How to Store

Store: Store muffins on a counter covered with linen towel or in a ventilated container for 1-2 days. After I recommend to freeze them.

Freeze: Bake and cool muffins completely. Place in resealable plastic bag, let the air out as you are sealing, and freeze for up to 3 months. Thaw on a counter for a few hours.

Serving: Top with a smear of butter or your favorite nut butter for a snack. You can also pop it into a microwave to warm up for a minute or so.

Storage Tip

For more muffin storage tips and tricks, check out my detailed posts how to store muffins and how to freeze muffins.

FAQs

Why are my zucchini muffins dry?

You either have not measured flour correctly or over baked the muffins. Be sure to spoon flour into a measuring cup and level with a knife rather than dunking it into a bag with flour. And bake muffins just until toothpick inserted in the center comes out clean.

Can I use yellow squash?

Yes, you can.