by Olena

Healthy Zucchini Muffins

Olena's image
Olena Osipov
4.9 from 16 votes

Healthy Zucchini Muffins are inspired by healthy zucchini bread and tested with 3 different flours – whole wheat or spelt flour, gluten free flour and almond flour. Now everyone can enjoy!

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!

healthy zucchini muffins on a cooling rack

Zucchini Muffins

These healthy zucchini muffins will fuel your body for the day. They are moist, fluffy, and tested with 3 different flours: whole wheat flour (spelt), gluten-free flour, and almond flour.

Baking healthy muffins is one of my favorite things to do. Because these little breads qualify as a healthy breakfast or snack, kids can grab them for school and as a mom, I know kids are not eating a lot of sugar and empty calories.

Plus, not only does the choice of flour impact the nutritional value, but the hidden zucchini within these muffins packs in moisture and nutrients without veggie flavor.

healthy zucchini muffins on a cooling rack

Ingredients for Healthy Zucchini Muffins

  • Zucchini
  • Egg (s)
  • Applesauce
  • Maple syrup or honey
  • Vanilla extract
  • Baking powder + soda
  • Whole wheat, spelt, gluten free or almond flour

ingredients for healthy zucchini muffins

#1 Whole Wheat Zucchini Muffins

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

While, spelt flour 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 healthy banana muffins, pancakes, cinnamon rolls, and chocolate zucchini bread!

  • Flour used: Sprouted spelt flour.
  • Batter consistency: Should be of regular muffin consistency – thicker than for pancakes but thinner than for cookies.
  • Changes to 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

  • Flour used: I had this gluten free flour from Bob’s Red Mill on hand and decided to give it a try. I have to say because flour is made from garbanzo and fava beans, it smells like beans. Muffins turned out surprisingly good and with very mild bean taste.
  • Batter consistency: Batter was quite more runny than traditional wheat flour muffin batter. I was a bit worried but it all worked out.
  • Changes to 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 choice but if you have to use gluten free flour or have other favorite brand, you will be golden.

bag of gluten free flour gluten free zucchini muffins batter in a bowl

#3 Almond Flour Zucchini Muffins

  • Flour used: Almond flour is one of my favorite flours of all times. 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 recipe: The change from whole wheat zucchini muffin recipe was 1 1/3 cups more flour and 2 extra eggs.

If you want to try more zucchini + almond flour combo, check out my lemon zucchini bread. It’s OMG melt in your mouth experience. You will think you are eating unhealthy Starbucks. I had to pinch my arm, for realz.

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 carrot cake. 

bag of almond flour on a counteralmond flour zucchini muffins batter in a bowl

How Long to Bake Muffins?

Baking time is the same for all 3 types of muffins – 22 minutes in preheated 350 F degrees oven.

What was your favorite?

healthy zucchini muffins 3 ways

How to Store and Freeze Zucchini Muffins

Storing: If you are baking zucchini muffins in summer and it is hot, I recommend to refrigerate muffins in airtight container for up to 5 days. In cooler months, store muffins in a container lined with 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 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

Healthy Zucchini Muffins with applesauce and 3 flour options. Whole wheat or spelt, gluten free and almond flour. Moist and fluffy.
4.88 from 16 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:

  • 2 cups grated zucchini packed and not squeezed
  • 1 large egg
  • 1/2 cup unsweetened applesauce
  • 1/2 cup honey or maple syrup
  • 1 tsp pure vanilla extract
  • 1/2 tsp cinnamon
  • 1 tsp baking soda
  • 2 tsp baking powder aluminum free
  • 1/4 tsp salt
  • 2 cups whole wheat or spelt flour
  • 1/2 cup chocolate chips nuts, blueberries etc.
  • Cooking spray I use Misto

Gluten free zucchini muffins:

  • 2 cups grated zucchini packed and not squeezed
  • 1 large egg
  • 1/2 cup unsweetened applesauce
  • 1/2 cup honey or maple syrup
  • 1 tsp pure vanilla extract
  • 1 tsp cornstarch
  • 1/2 tsp cinnamon
  • 1 tsp baking soda
  • 2 tsp baking powder aluminum free
  • 1/4 tsp salt
  • 2 3/4 cups gluten free flour
  • 1/2 cup chocolate chips nuts, blueberries etc.
  • Cooking spray I use Misto

Almond flour zucchini muffins:

  • 3 eggs large
  • 1/2 cup unsweetened applesauce
  • 1/2 cup maple syrup or honey
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 1 tsp pure vanilla extract
  • 1/4 tsp salt
  • 1 cup shredded zucchini not squeezed
  • 3 1/3 cups almond flour
  • 1/2 cup chocolate chips nuts, blueberries etc.
  • Cooking spray I use Misto


  • 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.


    Serving: 1muffin | Calories: 119kcal | Carbohydrates: 26g | Protein: 3g | Fat: 1g | Saturated Fat: 1g | Cholesterol: 14mg | Sodium: 243mg | Potassium: 169mg | Fiber: 3g | Sugar: 10g | Vitamin A: 61IU | Vitamin C: 4mg | Calcium: 73mg | Iron: 1mg
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    olena osipov in the studio

    Hello and welcome to iFOODreal.

    My name is Olena Osipov. I'm a mom to 2 boys, a wife to Alex and we reside on magical Vancouver Island in British Columbia, Canada. This is our healthy family recipes blog. Originally from Ukraine, I grew up on real food. As an adult, I struggled with diets for years because none worked long-term. Now for over 10 years, I cook easy healthy meals for my family. I can help you with “What’s for dinner?” too.

    37 comments on “Healthy Zucchini Muffins

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    1. 5 stars
      Made the almond flour version. I was a little skeptical but they were delicious! I halved the baked time and made some mini ones for my daughter. Thank you!

    2. 5 stars
      Best ever zucchini muffin recipe. Used almond flour and maple syrup. Cannot taste maple syrup at all. Just makes it taste as if sugar was used… but so much healthier! Wonderful filling breakfast or snack.

    3. 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?

      1. Hi Ella. At this point the plugin we use to enter recipes does not support metric measurements. They are working on it. Sorry for the inconvenience. And honestly I have not tried all applesauce. Not sure if it will turn out tasty and rise.

    4. 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!

    5. 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.

    6. 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. 🙂

    7. 5 stars
      Can I bake the almond flour muffins in a mini-muffin pan? If yes, how long and at what temp to bake them?
      The mini-muffin size is perfect to pack in a kids lunchbox. 🙂

    8. 5 stars
      This recipe was delicious!! Thank you so much for sharing.

      I used almond flour and blueberries. My husband even loved them!

    9. 4 stars
      Made the whole wheat flour version and followed recipe exactly. Batter was very thick and muffins turned out very dense. On the positive side they tasted great! Any suggestions on making batter less dry? Going to try almond flour next.

      1. Hmmm you can add 1/4 cup or a bit more applesauce to thin the batter and that should help with density. Did you flatten the top of measuring cup with flour? Wonder if too much flour…

    10. 5 stars
      Olena, amazing recipe! Our family loves these, we did the whole wheat version. We’ve made four batches in the last two weeks. Trying to get some in the freezer for easy breakfasts.

    11. 5 stars
      Hi Olena,

      Thanks for your recipes! I just made your banana muffins using GF flour and they were fantastic.
      For this recipe, if I don’t have applesauce (for the GF flour version), would mashed banana do?

        1. Hello! Just made you healthy zucchini bread and healthy lemon zucchini muffins, both are delicious!! Want to try these with lupin all-purpose flour, should I follow the GF recipe or the almond flour recipe? Thank you!

    12. Hi Olena,
      I noticed that in the ingredient listing using Almond Flour that both applesauce and cinnamon are missing.
      Was this on purpose, and why the batter is less runny? Or was it an omission?
      Thanks. Looking forward to trying the recipe. I, too, love Almond Flour!

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