Healthy Zucchini Muffins

You’re going to love these healthy zucchini muffins. They’re soft, moist, and filled with deliciously cozy flavors. But most importantly – they’re loaded with sneaky veggies!

Zucchini muffins spread out on a table

Perfectly soft n’ sweet zucchini muffins that are secretly healthy? Now that’s a baked good (and zucchini recipe) I can get by! All you really need are some baking essentials, plus a large handful of freshly grated zucchini to make this happen.

One thing to note is that these muffins aren’t overly sweet like ones you may have had at a bakery. Instead, I opted for a lightly sweetened, more netural flavor to make them versatile – like a slice of my paleo zucchini bread! That way you can enjoy these with a slab of butter or chia seed jam for something a bit more sweet. The choice is yours!

Ingredients for healthy zucchini muffins

What’s In These Healthy Zucchini Muffins

Like all my other muffins recipes, you’ll need a set of dry ingredients and wet ingredients, plus one large zucchini.

Dry Ingredients:

  • Almond Flour, Tapioca Flour & Coconut Flour: This triumvirate of flours is my signature blend for a light and fluffy texture (that’s secretly gluten-free!).
  • Baking Soda: Just a pinch to help these muffins rise properly.
  • Cinnamon, Nutmeg & Salt: Gives that subtle spiced flavor that’s irresistible in baked goods.

Wet Ingredients:

  • Eggs: Just 3 large eggs are need here.
  • Applesauce: This is a secret sweetener and it helps to keep the muffins extra-moist.
  • Maple Syrup: I prefer maple syrup as an all-natural sweetener, but you could use honey as well. Just note that honey tends to make baked goods a little heavier and denser.
  • Apple Cider Vinegar: This is needed for the chemical reaction with the baking soda to fluff the muffins up!
  • Grated Zucchini: I normally use a box grater, but a food processor with a grating tool works great as well.

Find the printable recipe with measurements below.

Holding half of healthy zucchini muffin

How To Make Healthy Zucchini Muffins

Once you’ve nailed the measurements of the batter – the rest of this recipe is easy. But before we do anything, lets get your oven preheated to 350°F and line a muffin tin with 10 muffin cups (yes 10, not 12). Then follow along below.

Start with the dry ingredients. Add the flours, baking soda, cinnamon, nutmeg, and salt to a mixing bowl and stir until combined.

Onto the wet ingredients. In a separate bowl, whisk together the eggs, applesauce, maple syrup, and apple cider vinegar. Squeeze the grated zucchini in a nut milk bag or kitchen towel to remove excess water. Then stir the grated zucchini with the wet ingredients.

Mix together, fill the muffin cups, and bake! Pour the wet ingredients into the dry and stir until the batter is completely mixed. Evenly divide the batter between the muffin cups. Then bake the zucchini muffins for about 28-32 minutes. Make sure to do the toothpick test to see if they’re done!

Baking zucchini muffins in a tin tray

Tips For The Best Zucchini Muffin Recipe

  • It’s crucial to get the moisture out of the zucchini! Otherwise your muffins will have a soggy texture (and that’s not good). So make sure to give your grated zucchini a good firm squeeze!
  • Smooth out the top for a more clean surface. I left mine as is when I spooned them into each tin space, giving it a more crumble like topping. But you can smooth it out with the back of a spoon so that it bakes into a round top.
  • It’s better to slightly over-bake rather than under-bake. There’s lots of moisture in these muffins, so it’s best to err on the side of extra golden. Trust me, they’ll still be moist inside!

A Few Storage Options

These zucchini muffins are best when they’re slightly cool, but still warm from the oven. That’s my favorite!

  • To store: You can leave them at room temperature for 2 to 3 days. After that, store them in the fridge for about one week in an airtight container.
  • To freeze: Place them in a freezer-safe container for up to 3 months. When you’re ready to enjoy, thaw them in the fridge or at room temperature.
Zucchini muffins on a metal tray next to a napkin

More Zucchini Recipes You’ll Love

Zucchini season is here, which means it’s time to get creative in the kitchen with my favorite veggie! Here’s a few ideas for you:

If you make these healthy zucchini muffins, let me know how they turned out! I’d love to hear what you think in the comments below.

A few healthy zucchini muffins next to a napkin.

Healthy Zucchini Muffins

5 from 6 votes
Prep Time: 20 mins
Cook Time: 25 mins
Total Time: 45 mins
Servings: 12 servings
Author: Lisa Bryan
Healthy zucchini muffins that are soft, moist, and filled with deliciously cozy flavors. But most importantly – loaded with sneaky veggies! Watch the video above to see how I make them.


Dry Ingredients

  • 1 ½ cup almond flour
  • ½ cup tapioca flour
  • ¼ cup coconut flour
  • 1 teaspoon baking soda
  • 2 teaspoon cinnamon
  • ½ teaspoon nutmeg
  • ½ teaspoon salt

Wet Ingredients

  • 3 eggs
  • ½ cup applesauce
  • ¼ cup maple syrup
  • 1 tablespoon apple cider vinegar
  • 1 ½ cup grated zucchini


  • Preheat the oven to 350F and line a 12-serving muffin tin with muffin cups. Then add all of the dry ingredients to a mixing bowl and stir until combined.
    Stirring ingredients for healthy zucchini muffins in a bowl
  • In a separate bowl add the eggs, applesauce, maple syrup, and apple cider vinegar and whisk together. Squeeze the grated zucchini (really firmly) in a nut milk bag or kitchen towel to remove the excess water. Then add the grated zucchini to the wet ingredients and stir to combine.
    Whisking together ingredients in a bowl for healthy zucchini muffins
  • Pour the wet ingredients into the dry and stir until the batter is well mixed. Evenly divide the batter between the muffin cups.
    Adding healthy zucchini muffin batter into a muffin tin.
  • Bake the zucchini muffins for 28-32 minutes or until a toothpick comes out clean.
    Healthy zucchini muffins on a marble table.

Lisa’s Tips

  • This is the nut milk bag I use to squeeze the zucchini and I love it. It’s great for homemade almond milk as well.


Calories: 149kcal, Carbohydrates: 15g, Protein: 5g, Fat: 8g, Saturated Fat: 1g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 1g, Cholesterol: 41mg, Sodium: 211mg, Potassium: 82mg, Fiber: 3g, Sugar: 6g, Vitamin A: 94IU, Vitamin C: 3mg, Calcium: 49mg, Iron: 1mg
Course: Breakfast
Cuisine: American
Keyword: Healthy Zucchini Mufins, Zucchini Muffin Recipe, Zucchini Recipe
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24 comments on “Healthy Zucchini Muffins”

  1. I am not gluten free but have recently discovered through my naturopath who did metabolic testing on me that I need to be wheat, potatoe and yeast and cane sugar free. This includes tapioca, xantham gum and guar gum. Do you know a flour blend I could use for this recipe? And for breads in general? Really love your recipes and have been helped so much by your channel/blog. Thanks

  2. Could you just use a gluten free flour instead of this blend? It’s too hard to find all these and also expensive but I do have gluten free flour. Thank you!

    • I haven’t tried this with just a gluten-free flour blend, but I know you can replace tapioca flour with it. Otherwise, if you test it out, let me know how it goes!

  3. Love this recipe! I used a hamburger patty press to squeeze out the zucchini… way easy on the hands with RA!5 stars

  4. I’ve made this recipe twice now and the muffins are absolutely delicious!  I am trying to avoid almonds so used tigernut flour instead of almond flour and the recipe turned out great!5 stars

  5. What can i sub for applesauce?  Does it serve as a sweetener or is it texture too?
    I was going to try honey but wondering about texture

  6. I have a love/hate relationship with these muffins. I ate them all so it must have been more love than hate. :D I loved the flavor and overall texture of them, however, I can always point out the coconut flour in any baked good due to the texture. That is the only thing I did not like about them. Perhaps I could substitute it for some more almond flour? Also, I personally think it needs just a touch more sweetness. Maybe adding a small amount of dried fruit to it would have made it perfect for my tastes. Thanks for the recipe, Lisa!

    • I always find this trio of flours to create the perfect texture, but you can try subbing it with almond flour to see what happens. Do let me know if you try! And as for the sweetness level, you can add a smidge more maple syrup (or dried fruit works too!).

  7. I’m currently sitting up in bed eating one of these muffins, which I baked earlier in the day. I am in utter shock at how perfect & delicious these are, considering there is no fat/oil added. They are so moist & have a beautiful fluffy texture! The cinnamon & nutmeg is just such a classy touch too! I added 1/3 cup of organic sultanas just for the little extra pop of goodness. Perfection!!!5 stars

  8. OMG… easy directions and oh sooo good! Thank you for always providing directions with tips and explanations- love your site! These muffins  are a definite rotation for breakfast and snacks! 5 stars

  9. I made these and they turned out amazing! Delicious and filled with veggies. Me and my husband loved them. But could they be made with equal amounts of grated carrots or apples? My toddler wasn’t a fan of the “green bits”. Loved this recipe!5 stars

    • I haven’t tried with grated carrots or apples. But could potentially work! If you try it, let me know how it goes :)

  10. I made these with raisins and nuts. Everyone loved them!5 stars

  11. Can I use all oat flour or regular flour?

    • I haven’t tested this with oat flour. But if you’re looking to use AP flour, I would just search for a regular zucchini muffin recipe :)

  12. Can I use all-purpose-flour instead of gluten-free ones?