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 healthy lemon 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 and taste amazing!

Baking healthy muffins is one of my favourite 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. Homemade muffins are so much healthier than anything you’d buy at the store because they are made with pure and simple ingredients without all the extra junk.

This recipe focuses on wholesome ingredients that pack a nutritious punch. Whole wheat or spelt flour adds both protein and fiber, applesauce replaces heavy oils, while maple syrup keeps these refined sugar free!

Five zucchini muffins with one unwrapped with a bite missing.

Why You’ll Love This Healthy 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 oil consumption.
  • Veggies: A full 2 cups of zucchini in 12 muffins means you are getting an extra serving of veggies!

Ingredients You Will Need

Zucchini, whole wheat flour, applesauce, maple syrup, oil, vanilla extract, eggs, cinnamon, baking staples, oil.

The best part about making healthy zucchini muffins, is most of the ingredients you probably already have on hand in your fridge and pantry!

  • Zucchini: You will need a full two cups of shredded zucchini, that has not been squeezed!
  • Eggs: Used for binding and just so happens to add nutrients, too!
  • Applesauce or yogurt: Sweetened or unsweetened. Use any yogurt like plain regular yogurt or Greek yogurt. Generally 2% fat and higher will yield better results.
  • 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 + soda: Used to give and to create a light and airy texture, avoiding heavy and dense muffins. Find aluminum free baking powder, if you can.
  • Whole wheat flour: Regular whole wheat or spelt flour is best, see Substitutions for gluten free flour.
  • Optional add-ins: Chopped walnuts, add crunch, antioxidants and protein.

How to Make Healthy Zucchini Muffins

A few easy steps, one bowl and you are well on your way to making your healthy zucchini muffins recipe!

Shredded zucchini on a plate with a box grater.

Prep: Shred zucchini using a box grater. Do not squeeze. Prep and spray muffin tin. Set aside.

I like to use largest holes of the grater so you can see those pretty green speckles of zucchini. You can also use smaller hole side “to hide” the veggies.

Eggs, maple syrup, applesauce and baking staples in bowl with a blue whisk.

Mix: Add eggs, applesauce, maple syrup, oil, vanilla extract, cinnamon, baking powder, baking soda and salt to large mixing bowl. Whisk well to combine.

Make sure to whisk until no small lumps of baking powder and soda are left.

Flour being stirred with spatula in bowl of muffin batter.

Stir in flour: 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. The batter will thicken as dry ingredients absorb moisture.

Be careful to stir just until your muffin batter is combined. Over mixing will cause your zucchini muffins to be dense.

Zucchini on top of muffin batter in a bowl.

Fold in zucchini: And optional walnuts, stir gently until just incorporated.

Muffin batter in blue muffin tin.

Bake muffins: Distribute batter evenly between 12 openings of a muffin tin and bake for 20 minutes or until a toothpick inserted in the center comes out clean.

Use a regular ice cream scoop to easily fill your muffin pan and distribute batter evenly.

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.

Optional Mix-In’s and Substitutions

  • Nuts or fruit: Add up to 1/2 cup of chopped walnuts, pistachios, or slivered almonds. Fresh or frozen blueberries, dried raisins, or mini chocolate chips would be great as well!
  • 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. Yogurt will also work.
  • 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 tsp 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 egg or chia egg.
Healthy zucchini muffins with a bowl of shredded zucchini.

How to Pick a Zucchini for Muffins?

Pick a firm zucchini that it not too soft, that could be a sign it is starting to go bad.

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.

How to Shred 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.

My preferred method is to shred the zucchini using a box grater (also called cheese grater). You could use a food processor, but be careful not to over shred your zucchini, or it will be a watery mess. Use the pulse function to avoid this happening.

Do I Need to Squeeze Excess Water From Zucchini?

Do not squeeze out excess water. There are some recipes that will require you to squeeze the excess moisture out of a zucchini muffin recipe but this is not one of those times because the moisture is needed.

Why Are These Muffins Considered Healthy?

As always, the answer “healthy” is relative. These healthy zucchini muffins are made with wholesome ingredients, unrefined sugars, and include a vegetable!

There are major nutritional benefits happening here plus by making them at home, there are no added preservatives, crazy sugars, sodium, or other items of that junky nature.

Is it ok to eat an entire tray of “healthy” muffins in one sitting? No, but a muffin or two throughout the day is definitely a healthy way to enjoy a protein packed snack.

Storing and Serving Options

Storing healthy zucchini muffins: Refrigerate muffins in an airtight container for up to 5 days.

Freezing healthy zucchini muffins: To freeze muffins, bake and cool. Place in resealable plastic bags, 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, or for a complete brunch spread serve with vegetable frittata.

More Healthy Muffins Recipes

Browse my favorite healthy muffin recipes for lots more inspiration! Alternately, you may also love these healthy zucchini recipes!

Healthy zucchini muffins stacked on top of each other with one unwrapped from liner.
Healthy zucchini muffins some stacked with a fresh zucchini.

Healthy Zucchini Muffins

Healthy Zucchini Muffins are easy to make in one bowl and super delicious! They are light, fluffy and moist.
4.96 from 46 votes
Servings 12 muffins
Calories 196
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes



  • Preheat oven to 375 degrees F and spray non-stick 12 muffin tin with cooking spray. Set aside.
  • In a large mixing bowl add eggs, applesauce, maple syrup, oil, vanilla extract, cinnamon, baking powder, baking soda and salt; whisk well to combine.
  • Add flour and gently mix until combined. Add zucchini and nuts (if using). Stir and do not over mix.
  • Distribute batter evenly between 12 openings of a tin (I used regular ice cream scoop) and bake for 20 minutes or until a toothpick inserted in the center comes out clean.
  • Let muffins cool for a few minutes and transfer to a cooling rack to cool off completely.



  • Recipe improved in June 2022 and here is almond flour zucchini muffins recipe from now on.
  • Store: Refrigerate in a glass airtight container for up to 5 days or freeze for up to 3 months.
  • Swap the applesauce: For the same amount of mashed bananas for a slightly different flavor. Or replace with yogurt.
  • No need to peel zucchini first. The skin is thin, light, and edible.
  • 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 tsp cornstarch.


Serving: 1muffin | Calories: 196kcal | Carbohydrates: 26g | Protein: 5g | Fat: 9g | Saturated Fat: 1g | Trans Fat: 0.003g | Cholesterol: 27mg | Sodium: 143mg | Fiber: 3g | Sugar: 10g
Course: Muffins
Cuisine: North American
Author: Olena Osipov
Did you make this recipe?Mention @ifoodreal or tag #ifoodreal!

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About Olena

Welcome! I grew up in Ukraine watching my grandma cook with simple ingredients. I have spent the last 11 years making it my mission to help you cook quick and easy meals for your family!

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  1. 4 stars
    I love these muffins!! However I always find that I have about Half a cup to a cup of whole wheat flour extra. I have been baking for years. And know how to measure everything exactly. I do not squeeze out the zucchini after grating and measure it just as you said. So I just add a few splashes of milk and the recipe turns out fine every time. I have no idea why I always have flour left over.
    I add chopped walnuts and mini chocolate chips to the recipe. I also take this into consideration when counting the calories. These muffins are absolutely delicious! And so moist!
    I have followed your blog four quite some time now and only had one recipe that I really didn’t care for. The rest are great! I really appreciate your healthy recipes.

  2. 5 stars
    I made the wheat version. They were really moist but I would recommend more cinnamon, and either apples or bananas to add a little more natural sweetness than the honey. I will make these tweaks and try again.

  3. 5 stars
    I was a little skeptical but they were delicious! I halved the baked time and made some mini ones for my daughter. Thank you!

  4. 5 stars
    Best ever zucchini muffin recipe. Just makes it taste as if sugar was used… but so much healthier! Wonderful filling breakfast or snack.

  5. 5 stars
    Hello Olena.

    I’m from Ukraine, too, but I’m not sure if a Russian (or Ukrainian?) comment would be welcomed here. Anyways, may I ask you to specify metric measurements in the recipes above? It’s just such a pain to search for each ingredient to recalculate the recipe. Would greatly appreciate your help)
    And one more question: can I substitute the syrup or honey for more applesauce?

  6. 5 stars
    I’ve never been a fan of baking but this recipe was really easy to follow and Made incredibly moist and flavorful muffins. I hadn’t used almond flour before either, but now I’m hooked. They’re perfect protein packed power food for hiking and backpacking.
    I’ve made both chocolate chip muffins and also used the lemon zucchini bread recipe as muffins too. Both turned out great!

  7. Can you suggest some substitutions if I wanted to use protein powder in the batter? Would it go instead of something? It just dissolves in water so im not sure.

    1. HI Samantha. I have never tested this recipe with protein powder, so I can’t say for certain what would/wouldn’t work. Baking is a science.

  8. 5 stars
    I just made the whole wheat muffins and doubled the recipe. I’m glad I did. I added raisins and walnuts. They are delicious. Thanks once again Olena. I am so thankful to have found you. ?. We have enjoyed so many of your recipes.

    1. I just tested with gluten free flour. I have not tested with chickpea flour only so can’t do any recommendations. Feel free to try your favorite flour and report back. 🙂

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