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, carrot 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.

Storage Tip

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

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.
4.88 from 55 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. 5 stars
    I just made these for breakfast and am so impressed! They turned out moist and with the perfect touch of sweetness! Thank you for this healthy recipe. I’ll be making these again!

  2. 5 stars
    I love this recipe. I have an abundance of crookneck squash so used that instead of zucchini. I used applesauce and honey and they came out perfectly golden and moist! My next batch I’ll use maple syrup and Greek yogurt. The nuts were a nice addition too. I’m happy to have found this yummy recipe and will be baking a new batch soon! Delicious!

  3. Could you substitute 1/2 c crushed pineapple for the honey or maple syrup? Just trying to cut more sugar and calories. I skipped the nuts and used Greek yogurt in place of the oil to skimp on calories too. They turned out great.

    1. Hi Barb, the recipe has not been tested as such but if you try let us know. You could also try a sugar free syrup.

  4. 5 stars
    I made the muffins and used frozen shredded zucchini (slightly drained). Overall these were super good and my kids kept asking for more!

    1. So glad you enjoyed them! Thanks for letting us know how they turned out. I do wonder if the frozen shredded zucchini may have needed to be squeezed just a tiny bit just as frozen tends to be more watery but sounds like it all worked out in the end and the kids were happy (best compliment, right?!) 🙂

  5. 5 stars
    I love these muffins. My sister in law who is celiac also loved them. My family with no gut issues also love.
    They are for everyone. Thankyou for your sharing Melanie

  6. I made the gluten free version using Bob Hills gluten free Baking flour. I could not even get the batter mixed. Way too much flour. Perhaps baking flour is different than gluten free all purpose flour. I added another egg – 1/4 cup apple sauce plus 1/3 cup frozen blueberries just the try and moisten the mixture. They are currently in the oven. I have enough batter for at least another 4 muffins which means the recipe yields 16 muffins. I measured everything and made sure ingredients were level before adding. Any ideas as to what’s went wrong?

    1. Yes, there is a difference in gluten free baking flour and gluten free all purpose flour – this recipe was only tested using gluten free all purpose flour – Bob’s Red Mill as noted, sometimes even brands of gluten free flours can differ as well.

  7. 5 stars
    I’ve tried several zucchini muffin recipes in the last year and have even made batches which unfortunately were so bad I threw them all away (yikes – $$$). I tried this one today with the almond flour. This is the first time there was no squeezing water out of the zucchini. I was skeptical about how these would turn out by followed the instructions… After 22 minutes, I took them out of the oven. My first thought was, “dang, these look dense and are probably going to be dreadful.”
    But I HAVE GREAT NEWS! These are GREAT! PERFECT! I’m headed back to the store to buy more almond flour so I can make more (zucchinis this week are HUGE). I made one batch and then divided in half. Made 6 muffins with coconut flakes and mini chocolate chips. With the other half batch, I added blueberries and had enough batter for 8. I made them in normal size muffin pan but didn’t overfill, so the height was the height of the pan when they came out of the oven.
    THANK YOU so much! I FINALLY have a WONDERFUL and healthy zucchini muffin recipe 🙂 🙂 :). My husband just ate one and said, “these are great! The best ones yet!”

  8. 5 stars
    Superb! I’ll no longer fear friends who arrive bearing zucchini! More batches in store for the dark winter days.

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