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Healthy Zucchini Muffins | Gluten-Free, Vegan

by Capri Lilly
Published: Last Updated on

These Zucchini Muffins are moist, fluffy, flavorful and completely gluten, egg, and dairy-free. This is an easy, healthy zucchini muffin recipe that gives you perfectly baked muffins every time: made with gluten-free all-purpose flour and almond meal. No more gluten-free muffins that require 20 different flours and ingredients. Filled with blueberries and pecans, these vegan zucchini muffins are perfect for breakfast, a healthy snack, or a tasty dessert.


I love the versatility of zucchini. It’s such a dynamic vegetable and can be used to make bread, pasta, muffins, chips, you name it! These zucchini muffins are my favorite. I enjoy them for breakfast, as an afternoon snack, and even for dessert. My boyfriend loves them too! He told me, “They are the perfect muffins, moist and fluffy all the way through.”. He then laughed as he told me of a Seinfeld episode where Elaine explains that the muffin tops are better than the stump and later was lambasted by a homeless shelter administrator because everyone was complaining about the horrible stumps that were left at their facility. HAHA! We had a great laugh off of that. I bet Elaine would love these muffins— the top and the stump are great!

Curious about what zucchini muffins taste like?

Rest assured, zucchini muffins are a crowd pleaser to both children and adults alike. The zucchini taste is hardly detectable. If you were not told zucchini was in the muffins, you’d never know—outside of the green shredded bits, you’ll find inside the muffins. They simply provide a fluffy density to the muffins and add tons of beneficial nutrients!

The muffins get most of their incredible flavor from the cinnamon, nutmeg, and whatever add-ins you choose. Zucchini muffins are a great way to snack in a healthy, enjoyable way!

How to prepare zucchini?

The beauty of zucchini is that it is malleable, simple, and easy to use whether you are making pasta, bread, cakes, or muffins. To prepare the zucchini for these muffins all you need is a box grater. Simply shave 2-3 zucchinis until you have 2 cups of grated zucchini.

You will notice that the zucchini holds a lot of water. Before mixing the zucchini with the other ingredients, using a paper towel or cloth squeeze as much moisture out of the zucchini as you can. Don’t worry, no need to have Popeye the Sailor Man’s strength here, a simple squeeze or two is just perfect! 🙂


The main ingredients for these delicious zucchini muffins:

The “Flour” and the “egg”

The reason that this is one of the best, EASIEST gluten-free zucchini muffins recipes is because this recipe does not call for 5 different gluten-free flours, resting time, or anything complicated.

I love using Bob’s Red Mill Gluten-Free flour and find it works perfectly. You’ll see there are a few tablespoons of almond meal in this recipe as well. That helps to soak up any excess moisture.

To keep zucchini muffins vegan and egg-free, I use both flax egg and applesauce. the flax egg is a great binder and offers a ton of nutrients (omega-3 fatty acid, protein, fiber). The applesauce is perfect for keeping these muffins moist and fluffy. I highly recommend using them both for the best results.

The flax egg is very simple to make. take 1 tablespoon of ground flax and 3 tablespoons of purified water. stir this mixture together and let it sit for 10-15 minutes. I usually do this first and move on to preparing my other ingredients. when the flax egg is ready you will notice it is a nice gooey consistency.

Healthy Zucchini Muffin Mix-ins

The world is your oyster! And so are these muffins! You can add whatever you’d like to the batter to make whatever flavor profile you fancy. Here are a few suggestions:

  • 1 cup Blueberries and  ½ cup Pecans: I used these to make tasty, healthy muffins that I can enjoy for breakfast or as a snack! (I prefer to use fresh blueberries instead of frozen blueberries, which tend to retain more water)

  • ½ cup Chocolate Chip: An all-time favorite. Using chocolate chips is a great way to create a healthy indulgent snack! Who knew vegetables and chocolate could taste so good!

  • ½ cup to 1 cup Dried Fruit: Raisins, Goji Berries, Coconut Shavings, Dried Mango (chopped), Dried Apricot (chopped) are all great options! Simply start with a half cup and add more as desired.

  • Chocolate (Cacao) Cream Icing: A tasty icing made with cacao, avocados, and maple syrup. A perfect rich, chocolatey icing that is refined sugar-free and a healthy complement to your zucchini muffins.


How to Store the Zucchini Muffins?

Good luck having any of these delicious muffins left! If you do have a few left, or make a double batch, these muffins hold up great!

If you are enjoying them within a few days of making the muffins, it is best to store the muffins in an airtight container and leave them on your kitchen counter. If you want them to last just a bit longer, you can store them in the fridge for up to a week.

Also, if you want to freeze them for a later date, these zucchini muffins freeze extremely well. Simply put them in a freezer-proof bag and they can be stored for up to 2 months. When you are ready to enjoy them, thaw them in the microwave for ~30 seconds or leave them on the countertop. You’ll be happy to see they taste just as great as when you first made them!


healthy zucchini muffins

Healthy Zucchini Muffins

These Zucchini Muffins are moist, fluffy, flavorful and completely gluten, egg, and dairy-free. Filled with blueberries and pecans, these vegan zucchini muffins are perfect for breakfast, a healthy snack, or a tasty dessert.
5 from 14 votes
Print Pin Rate
Course: Breakfast, Dessert, Snack
Cuisine: American, Healthy Options, Vegan
Prep Time: 20 minutes
Cook Time: 30 minutes
Total Time: 50 minutes
Servings: 12 muffins
Calories: 145kcal
Author: Capri Lilly


  • 1 1/2 cup All Purpose Gluten-Free Flour
  • 1/2 tsp Baking Soda
  • 2 tsp Baking Powder
  • 1 1/4 tsp Cinnamon
  • 1/4 tsp Sea Salt
  • 2 cups Grated Zucchini
  • 3 tbsp Coconut Sugar
  • 1 tsp Apple Cider Vinegar
  • 1/4 cup Maple Syrup
  • 1/4 cup Coconut Oil, melted
  • 1 tbsp Ground Flax
  • 1 tsp Vanilla Extract
  • 3 tbsp Water
  • 1/4 cup Applesauce
  • 3 tbsp Almond Meal

Optional Mix-Ins:

  • 1 cup Blueberries
  • 1/4 cup Pecans


  • Preheat the oven to 350°F. Place muffin liners into a standard, 12-muffin pan. Set aside.
  • Prepare the flax egg: Combine 1 tbsp ground flax with 3 tbsp purified water, mix well, and let sit for 10-15 minutes.
  • Using a grater, shred 2-3 zucchinis until you have 2 cups of shredded zucchini. Set aside.
  • Combine all the dry ingredients (except the almond meal) into a large mixing bowl.
  • Using a paper towel or clean cloth, gently squeeze the liquid from the zucchini. (You should have 1/4 cup liquid drained). In a separate large mixing bowl, combine the liquid ingredients and zucchini and mix well.
  • Slowly add the dry mix to the zucchini mixture. After the ingredients are fully combined, add 1-3 tablespoons of almond meal as needed to absorb any excess moisture.
  • Fold in your choice of mix-ins. Then evenly distribute batter among muffin tins, filling about 3/4 of the way full.
  • Bake for 25-30 minutes or until toothpick inserted into the middle of the muffin comes out clean.
  • Remove from the oven and allow the muffins to cool inside the muffin tin for 10 minutes then remove muffins and transfer to wire rack to finish cooling for 5-10 minutes.


Nutrition (1 of 12 Muffins):

  • Serving: Makes 12 Zucchini Muffins
  • Calories: 145
  • Fat: 6.2g
  • Cholesterol: 0mg
  • Carbohydrates: 22.5g
  • Sugar: 9.5g
  • Protien 2.3g


  • Store muffins in an airtight container on the kitchen counter and Enjoy for up to 3 days.
  • Store the muffins in an airtight container and place in the fridge to enjoy for up to a week
  • Muffins can be frozen; individually wrap muffins in ziploc bags or store them in a large freezer bag. Reheat for 30-45 seconds in the microwave or thaw them at room temperature.


Calories: 145kcal

Disclaimer: Some of the links above are affiliate links, which pay me a small commission for my referral at no extra cost to you and helps me keep my site running! I’m sharing these products because I use them, trust them, and cannot recommend them enough. All thoughts and opinions are 100% my own

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Renee April 16, 2020 - 11:11 am

5 stars
I’ve always loved zucchini bread and I can’t wait to try this!

GiGi Eats April 16, 2020 - 12:05 pm

5 stars
I see zucchini being used in baking all the time yet for SOME REASON I have still yet to incorporate it into mine! THIS needs to change ASAP!!! Thank you for the reminder 🙂

Hans David April 16, 2020 - 12:11 pm

Thanks for this recipe. I will forward it to my vegan friends.

Kristi McAllister April 16, 2020 - 6:29 pm

5 stars
These look absolutely divine! I’m gluten free and I’m always looking for new recipes. Can’t wait to try these!

Capri Lilly April 16, 2020 - 10:11 pm

I am as well! I hope you like the recipe!

Sarah M April 18, 2020 - 6:52 am

Wow looking so yummy I think I should try this at home.

Jessica Collazo April 16, 2020 - 8:53 pm

5 stars
This recipe sounds very interesting I love zucchini and I adore hazelnut

Lavern Moore April 17, 2020 - 3:08 am

5 stars
This is a delightful recipe. I am looking forward to tasting!

Shelley at BeyondPennies April 17, 2020 - 5:30 am

5 stars
These zucchini muffins look delicious! I must try this recipe.

blair villanueva April 17, 2020 - 5:45 am

5 stars
Omg, now I am craving for muffins! I’ll share your recipe to my boyfriend and do this together 🙂

Capri Lilly April 19, 2020 - 9:35 pm

Hi Blair! That sounds like fun. I hope you enjoy!

Raksha N April 17, 2020 - 8:19 am

Wow I have never had Zucchini muffins. This looks great.

Steph April 17, 2020 - 8:23 am

This looks delicious.I have never tried zucchini but I will one of these days.

Natalia Vorche April 17, 2020 - 11:32 am

5 stars
Thanks for the prefect recipe I can’t wait to try this

Capri Lilly April 19, 2020 - 9:33 pm

You’re Welcome, Natalia! Hope you like!

aisasami April 17, 2020 - 2:58 pm

5 stars
Zuccini muffins sound AMAZINGLY delicious! I want to try making this!

Capri Lilly April 19, 2020 - 9:33 pm

It surely is! I love having them for breakfast with my tea!

Chirpybrains April 17, 2020 - 4:29 pm

5 stars
Wow, this looks so tasty and healthy! I’m trying this very soon.

Desiree April 17, 2020 - 6:31 pm

I’m not vegan but I’ll certainly try these zucchini muffins

Capri Lilly April 19, 2020 - 9:32 pm

That’s great! I’d love to hear what you think!

Anita April 17, 2020 - 7:27 pm

5 stars
These look delicious. Can’t wait to try them!

Capri Lilly April 19, 2020 - 9:31 pm

I hope you like!

mainak biswas April 18, 2020 - 5:47 pm

5 stars
Looks sooo yummy… will definitely try them out!

Capri Lilly April 19, 2020 - 9:30 pm

Please do! They are so delicious!

Elizabeth O April 27, 2020 - 5:43 pm

Woah! I loved to try this muffins gluten free. It looks really good and yummy! For sure, my friend would like this.

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