by Olena

Healthy Zucchini Muffins

by Olena

5 from 3 reviews

Healthy Zucchini Muffins are inspired by my healthy zucchini bread but 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. Just like healthy banana muffins and banana zucchini muffins.

healthy zucchini muffins on a cooling rack

Healthy Muffins

Baking healthy muffins is one of my favorite things to do. Because these little breads qualify as healthy breakfast or a snack, kids can grab for school and I can fuel my body for the day.

I struggle with healthy breakfast, honestly. Many times it’s toast or plain yogurt.

These healthy zucchini muffins with applesauce came out moist and fluffy. And because I know you guys well, I tested healthy zucchini muffin recipe with 3 different flours:

  • Whole wheat flour (spelt flour would work too)
  • Gluten free flour
  • Almond flour

Read till the end to find out our favorite.

healthy zucchini muffins on a cooling rack

Ingredients You Will Need

  • Zucchini
  • Egg (s)
  • Applesauce
  • Maple syrup or honey
  • Vanilla extract
  • Baking powder + soda
  • Your choice of flour

ingredients for healthy zucchini muffins

#1 Whole Wheat Flour

healthy whole wheat flour zucchini muffins batter in a bowl

Spelt flour or whole wheat flour is my choice for making healthy muffins.

It has added benefits of fiber, vitamins and nutrients that all-purpose flour doesn’t have. We love whole wheat muffins’ texture.

Whole wheat zucchini muffins is the base for this recipe. Dough should be of regular muffin consistency – thicker than for pancakes but thinner than for cookies.

I will walk you through the changes with other flours.

#2 Gluten Free Flour

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

I had this gluten free flour from Bob’s Red Mill on hand and decided to give it a try.

Batter was quite more runny than traditional wheat flour muffin batter. I was a bit worried but it all worked out.

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.

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.

I had to use 3/4 cup more flour plus 1 tsp cornstarch vs. whole wheat zucchini muffins.

#3 Almond Flour

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

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 was something in between whole wheat and gluten free. Not as thick but not as runny either.

If you want to try more zucchini + almond flour combo, check out my healthy 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.

The change from whole wheat zucchini muffin recipe was 1 1/3 cups more flour and 2 extra eggs.

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 Our Favorite?

The spelt flour (whole wheat) zucchini muffin.

Kids claimed it to be the best. Me and Alex were torn between spelt and almond flour muffins. I told you I am obsessed with almond flour. Muffins coem out so moist and tender.

What was your favorite?

healthy zucchini muffins 3 ways

How to Freeze Zucchini Muffins

Obviously, 36 muffins is a bit too many even for us.

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.

Craving More Healthy Muffins?


Healthy Zucchini Muffins

5 from 3 reviews

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

  • Author: Olena of
  • Prep Time: 10 minutes
  • Cook Time: 22 minutes
  • Total Time: 32 minutes
  • Yield: 12 muffins 1x
  • Category: Muffins
  • Method: Oven
  • Cuisine: North American


With whole wheat or spelt flour:

  • 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)

With gluten free flour:

  • 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)

With almond flour:

  • 3 eggs, large
  • 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)


  1. Preheat oven to 350 degrees F and spray non-stick 12 muffin tin with cooking spray. Set aside.
  2. 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.
  3. Add flour (and cornstarch for GF muffins) and gently mix until combined. Add zucchini and chocolate ships. Stir and do not over mix.
  4. 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.
  5. 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 1 week or freeze for up to 3 months.

 Did you make this recipe? Please give it a star rating in the comments.

olena osipov in the studio

Hello and welcome to iFOODreal.

My name is Olena Osipov. I'm a mom to 2 boys and a wife to Alex. And this is our healthy family recipes blog. I grew up in Ukraine on real food. As an adult, I tried many diets without results. Now for over 10 years, I cook quick and easy healthy meals for my family. I can help you with “What’s for dinner?” too.

What You Will Find Here

Healthy family recipes with simple ingredients. Many are inspired by my Ukrainian heritage. I share mostly dinner recipes because it just never ends... I’m obsessed with healthy freezer meals. And more than in love with my Instant Pot.

A Little More About Me

Originally from Ukraine, I now reside on magic Vancouver Island in British Columbia, Canada with my family. I started this blog in 2012 when I ended up at home with 2 small kids unemployed and a wee bit chubby.

14 comments on “Healthy Zucchini Muffins

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  1. 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…

  2. 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.

  3. 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!

  4. 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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