by Olena

Healthy Zucchini Muffins

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Olena Osipov
4.9 from 20 votes

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These Healthy Zucchini Muffins are inspired by my healthy zucchini bread and the results are amazing! Light, fluffy, moist muffins loaded with flecks of zucchini and sweetened with maple syrup! They were tested with 3 different flours – whole wheat spelt flour, gluten-free all-purpose flour, and almond flour. Each had results that were spectacular. This easy-to-follow recipe includes tips for all three versions!

Moist, fluffy, and full of fiber, these healthy zucchini muffins with applesauce are on our regular rotation with blueberry muffins, lemon zucchini muffins, and almond flour banana muffins! Having protein-packed baking on hand is a great way to ensure my family has loads of healthy snacks to choose from. It makes grazing fun and guilt-free!

healthy zucchini muffins on a cooling rack

Healthy Zucchini Muffins – No Refined Sugar!

Baking healthy muffins is one of my favourite ways to make sure my kids are eating a healthy breakfast or healthy snacks even in a rush! It comforts me as a mom, to know that my kids are not eating a lot of sugar and empty calories when they grab-n-go.

Of course, not all muffins are created equal. 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 was tested with whole wheat spelt flour, gluten-free flour, and almond flour and they all turned out great. Not only does the choice of flour impact the nutritional value, but the remaining ingredients do too.

You might wondering, isn’t a zucchini muffin recipe healthy just because it has zucchini in it? The short answer is no. If you overload it with sugars, and bad fats, and all kinds of additives and preservatives, a handful of shredded zucchini isn’t going to save you. It’s all encompassing so all the ingredients need to work together!

The hidden zucchini pack in the moisture, thanks to the water content that zucchini naturally carries. The unsweetened applesauce not only adds to the moisture, but gives it a warming subtle flavour of apple, and it is naturally sweetened with maple syrup, which also has nutritional value such as vitamins and antioxidants.

Having a tray of freshly baked muffins, like these healthy zucchini bread muffins, is something your kids will love coming home to after activities. They are moist, soft, and irresistible! Whether your family starts the day with one to fuel them for the day or ends the day with a muffin and a cozy cup of tea, these delicious muffins will be a hit. Good luck stopping at just one!

Why This Zucchini Muffin Recipe Works

  • These muffins are delicious, soft, moist and so easy to make!
  • Ready to eat in about 30 minutes which is perfect for busy mornings.
  • Freezer friendly which means you can bake lots and freeze some for later.
  • They’re packed with nutrients, and loaded with zucchini.
  • Baking with zucchini is a great way to use it up in a non “vegetable side dish” kind of way!
  • You can’t taste the zucchini!
  • Kids love them as a snack or breakfast and they are great for packing in school lunches.
  • They can be made with 3 different flour choices that all result in great-tasting muffins.
healthy zucchini muffins on a cooling rack

Ingredients for Healthy Zucchini Muffins

  • 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 healthy but this is not one of those times because the moisture is needed.
  • Egg (s): Used for binding and just so happens to add nutrients as eggs do! Need egg free? Readers have had success with flax/chia egg.
  • Applesauce: Unsweetened without the added sugar. Applesauce is a great alternative to using oil in any baking as well it adds a natural sweetness along with moisture.
  • Maple syrup or honey: Both pack a sweet punch and both will result in a slightly different taste. Either works in this recipe.
  • Vanilla extract: A warming note that rounds everything out nicely and adds a depth of flavour.
  • Cinnamon: A lovely spice that pairs well with applesauce, 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.
  • Salt: Brings out the flavours of the rest of the ingredients, enhancing the overall taste.
  • Whole wheat, spelt, gluten-free or almond flour: Depending on what your dietary needs and taste preferences are, you can decide which is best for you. Scroll down for information on working with all of them.
  • Optional add-ins: Keep it simple or add in some chocolate chips, nuts, or blueberries for added taste and texture.
  • Cornstarch: Needed only for all-purpose gluten-free muffins.
Spelt whole wheat flour, maple syrup, applesauce, zucchini, egg, baking staples.

3 Healthy Ways to Make Easy Zucchini Muffins (that taste amazing!)

#1 Whole Wheat Zucchini Muffins

Spelt flour or whole wheat flour is my preferred choice for making healthy muffins based on texture and taste.

If spelt flour is new for you, it is much healthier than regular AP but can be used in most of the same ways, with great lift and results every single time. Just like these whole wheat buttermilk pancakes, cinnamon rolls, and chocolate zucchini bread!

  • Flour used: Sprouted spelt flour (whole wheat works too).
  • Batter consistency: Should be of regular muffin consistency – thicker than for pancakes but thinner than for cookies.
  • Changes to the recipe: It is the base for this recipe. I will walk you through the changes with other flours.
healthy whole wheat flour zucchini muffins batter in a bowl

#2 Gluten Free Zucchini Muffins (all purpose)

  • Flour used: I had this all purpose gluten-free flour from Bob’s Red Mill on hand and decided to give it a try. I have to say because the flour is made from garbanzo and fava beans it also smells like beans. However, the muffins turned out surprisingly good and with a very mild bean taste.
  • Batter consistency: Batter was runnier than with traditional wheat flour muffin batter. I was a bit worried but it all worked out.
  • Changes to the recipe: I had to use 3/4 cup more flour plus 1 tsp cornstarch vs. whole wheat zucchini muffins.

Gluten-free zucchini muffins would not be my first choice but if you have to use gluten-free flour or have another favourite brand, you will be golden.

#3 Almond Flour Zucchini Muffins (also gluten-free)

  • Flour used: Almond flour is one of my favorite flours of all time. Just look at the ratings of almond flour banana muffins. I can’t believe how popular that recipe has become! Almond flour is moist and makes muffins very tender.
  • Batter consistency: Batter consistency was something in between whole wheat and gluten-free. Not as thick but not as runny either.
  • Changes to the recipe: The change from the whole wheat zucchini muffin recipe was 1 1/3 cups more flour and 2 extra eggs. There is no gluten to bind the muffins and create structure, so the added flour and eggs helped to combat that.

If you want to try more zucchini + almond flour combos, check out my lemon zucchini bread. It’s an OMG melt-in-your-mouth experience, kind of like eating something unhealthy from Starbucks, except without the guilt!

Almond flour has become one of my new favorite ingredients for baking with its ability to yield tender, moist, fluffy baked goods like almond flour brownies, pancakes, banana bread, and gluten free carrot cake

How to Make a Quick and Easy Batch of Zucchini Muffins

  • Preheat the oven and spray the muffin tin. Set aside.
  • Whisk eggs in a large mixing bowl for 15 seconds.
  • Add remaining ingredients minus the flour. The applesauce, maple syrup, vanilla extract, cinnamon, baking powder, baking soda, and salt. Whisk well to combine.
  • Add flour (and cornstarch for gluten-free all-purpose flour muffins) and gently mix until combined.
  • Toss in the zucchini and optional chocolate chips if you’re using and just stir to combine. You don’t want to over mix, which will create dense muffins.

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

  • Bake muffins for approximately 22 minutes or until a toothpick inserted in the middle comes out clean and allow the muffins to cool before transferring to a wire rack to cool completely.

Tips for Best Zucchini Bread Muffins

  • How Long to Bake Muffins? Baking time is the same for all 3 types of muffins – 22 minutes in preheated 350 F degrees oven.
  • Half the bake time for mini muffins for little hands!

Make mini muffins by reducing the baking time in half!

  • Grease your muffin tin using cooking spray. I use Misto, which is an olive oil spray.
  • Shred the zucchini using a grater, but don’t squeeze out any of the water.
  • It’s important to measure the ingredients as listed for optimal results. Level the flour so you’re not using too much. Remember, baking is a science.
  • Add in nuts for added protein. Walnuts, pistachios, and slivered almonds would be great. Of course, if you’re using almond flour, the extra almonds might be too much. Instead, you could try blueberries, raisins, or chocolate chips!
  • Swap the applesauce for the same amount of mashed bananas for a slightly different flavour. They will act the same way by providing moisture and replacing the oil but will give off a bit of a different taste.
  • No need to peel 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.

What was your favorite version? I would love to hear your thoughts!

Serving Recommendations

Zucchini muffins are great for breakfast or snack. Serve with these items!

Alternately, check out these healthy breakfast meal prep ideas for more inspiration (and motivation) to start your day off with a nutrition boost! And if you love zucchini as much as I do, these zucchini recipes will be your favorite for every meal.

healthy zucchini muffins 3 ways


How long to bake zucchini muffins?

The great thing about this zucchini muffin recipe healthy is the bake time is the same no matter which type of flour you’ve chosen to use. Of course, you’ll want to keep an eye on them no matter what, as not all ovens are the same. The general rule of thumb for 12 regular-sized muffins, is a bake time of 22 minutes. If you’re baking mini muffins, you want to check at the halfway mark, but they should be done by about 18 minutes.

What is the best way to add zucchini to muffins?

Here’s the thing. Some people will tell you, you must squeeze the water out before adding it to the batter. The excess water that zucchini carries will obviously add moisture to your batter so this can be a slippery slope. If you are using ingredients that already carry a ton of moisture, such as milk or oil, you have leeway to squeeze out extra water. This recipe does not use either of those two things, so the added moisture is welcome. It really does depend on the recipe.

Are zucchini muffins healthy?

As always, the answer “healthy” is relative. They are made with pure ingredients, unrefined sugars, and include a vegetable! There are major nutritional benefits happening here for these healthy zucchini bread muffins. There is also the option of choosing which flour is right for you, and 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.

What makes healthy zucchini bread muffins light, fluffy and moist?

The magic happens based on the ingredients and the science behind the amounts used. This is why it is important to follow the directions closely, otherwise, you may end up with unfavorable results. The moisture from the zucchini itself, along with the applesauce, helps to keep it moist. The fluffy nature also comes from the baking powder and baking soda and depending on the flour used, this will determine how light your muffins turn out. No matter what, they’ll taste great!

Making This Muffin Recipe in Advance

Storing: If you are baking zucchini muffins in summer and it is hot, I recommend refrigerating muffins in an airtight container for up to 5 days. In cooler months, store muffins in a container lined with a double paper towel for up to 2 days on a counter or in a pantry. Preferably away from sunlight.

Freezing: 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.

More Healthy Muffins Recipes

Or you can see my full collection of healthy muffins and quick breads, for lots more inspiration!

Healthy Zucchini Muffins

Healthy Zucchini Muffins

These Healthy Zucchini Muffins are inspired by my healthy zucchini bread and the results are amazing! Light, fluffy, moist muffins loaded with flecks of zucchini and sweetened with maple syrup! They were tested with 3 different flours – whole wheat spelt flour, gluten-free all-purpose flour, and almond flour. Each had results that were spectacular. This easy-to-follow recipe includes tips for all three versions!
4.91 from 20 votes
Print Save Rate
Course: Muffins
Cuisine: North American
Prep Time: 10 minutes
Cook Time: 22 minutes
Total Time: 32 minutes
Servings: 12 muffins
Calories: 119kcal
Author: Olena Osipov


Whole wheat zucchini muffins:

Gluten free zucchini muffins:

Almond flour zucchini muffins:


  • Preheat oven to 350 degrees F and spray non-stick 12 muffin tin with cooking spray. Set aside.
  • In a large mixing bowl add egg(s) and whisk for 15 seconds. Add applesauce, maple syrup, vanilla extract, cinnamon, baking powder, baking soda and salt; whisk well to combine.
  • Add flour (and cornstarch for GF muffins) and gently mix until combined. Add zucchini and chocolate ships. Stir and do not over mix.
  • Distribute batter evenly between 12 openings of a tin (I used regular ice cream scoop) and bake for 22 minutes or until a toothpick inserted in the centre comes out clean.
  • Let muffins cool for a few minutes and transfer to a cooling rack to cool off completely.

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 flavour. 
    • No need to peel zucchini first. The skin is thin, light, and edible. 
    • Egg free: Try using flax egg or chia egg.
    • Add in nuts for added protein. Walnuts, pistachios, and slivered almonds would be great. Of course, if you’re using almond flour, the extra almonds might be too much. Instead, you could try blueberries, raisins, or chocolate chips!
    • Mini muffins: Cut baking time in half, check for doneness and either remove or add 1 -2 minutes extra time.
    See recipe post for additional notes and FAQs.


    Serving: 1muffin | Calories: 119kcal | Carbohydrates: 26g | Protein: 3g | Fat: 1g | Saturated Fat: 1g | Cholesterol: 14mg | Sodium: 243mg | Fiber: 3g | Sugar: 10g

    Recipes and images are a copyright of It is against the law to republish recipes without permission. Nutritional info is approximate.

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    52 comments on “Healthy Zucchini Muffins

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    1. 5 stars
      I made the almond flour version and used frozen shredded zucchini (slightly drained). I ended up having to keep adding time as the insides were still fairly wet. Total cooking time for me was about 30 mins. The tips were a little more brown but 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?!) 🙂

    2. 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

    3. 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.

    4. 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!”

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

    6. 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.

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