It’s our last official day of Zucchini Week, and I’m sending us forth in style with what may just be my very favorite zucchini recipe of them all: Healthy Zucchini Muffins.

muffin pan full of Chocolate Chip Banana Healthy Zucchini Muffins

These moist, fluffy muffins are made with wholesome ingredients and are appropriate for toddlers, adults, and everyone in between. Whole grain and sweetened naturally, they are healthy enough to leave you feeling virtuous and sustained.

Chocolate-chip-studded, tender, and lightly spiced, they’re also scrumptious enough to taste like a treat you’ll look forward to eating in the morning or tucking in with for a midafternoon pick-me-up.

If you have as much zucchini lying around as we do, muffins freeze well, so you can make a triple batch and stow them away for a later date. Perhaps later this winter when (and I know this is hard to imagine) decent zucchini is difficult to find and you really, truly miss it.

I consider myself both a muffin aficionado (see: Chocolate Zucchini Muffins, Banana Oatmeal Muffins, Applesauce Muffins, Healthy Blueberry Muffins, ALL OF THESE HEALTHY MUFFINS) and a zucchini baked good aficionado (see: Zucchini Banana Bread, Zucchini Cookies, Paleo Zucchini Bread, et al.), so coming up with what I can confidently state is the best ever healthy zucchini muffin recipe is not a business I take lightly.

Many a test batch later, here we are! THE BEST EVER HEALTHY ZUCCHINI MUFFINS.

This recipe is one I make often, and it has received dozens of glowing reader reviews.

To round out Zucchini Week, I’m resharing it today (with an added video!) in hopes that if you haven’t tried it yet, you will. OR that if you have tried it before, you’ll remember how much you enjoyed it and treat yourself to a fresh batch sometime very soon.

overhead image of Healthy Zucchini Muffins studded with chocolate chips

How to Make the Best Healthy Zucchini Muffins

This Healthy Zucchini Muffin recipe uses pantry staples and fresh produce. Here are the main pantry ingredients you’ll need to make it.

  • Whole Wheat Flour. These muffins are 100% whole grain, meaning they’re high in protein and fiber and will keep you full and happy for longer. I like to use white whole wheat flour because its taste is light and mild.
  • Honey. For natural sweetness and extra moisture.
  • Coconut Sugar (or light brown sugar). To give the muffins structure and a lighter texture. You can find coconut sugar in most grocery stores and online.
  • Baking Powder + Baking Soda. To help give the muffins those beautiful, tall domed tops.
  • Coconut Oil. You can also swap light olive oil if you prefer.

NOW, here’s what sets this Healthy Zucchini Muffin recipe apart. In addition to the shredded zucchini, this recipe also calls for mashed ripe banana!

2 speckled ripe bananas and 3 whole zucchini

Because mashed banana is both sweet and moist, incorporating it into the recipe allows us to use a lesser amount of both sugar and fat while still having fantastic results.

Unlike other healthy muffin recipes you may have tried, these zucchini muffins are fluffy, tall, and tender, NOT rubbery or gummy. In fact, I doubt you’ll even realize that what you are eating is healthy!

clear mixing bowl with shredded zucchini, chocolate chips, and mashed bananas

Healthy Zucchini Muffins Mix-Ins

We are a house divided on our Healthy Zucchini Muffin mix-ins.

  • Mini chocolate chips are my absolute fave. I love chocolate and zucchini together, and the mini ones really work their way into every single morsel.
  • Blueberries are Ben’s constant request. You can use fresh or frozen blueberries. (If using frozen, no need to thaw them first).
  • Walnuts. Both of us agree there, so 95% of the time, the walnuts make it in.

This recipe is also fantastic all on its own, with or without the chocolate, nuts, etc. Feel free to go whichever route your household most enjoys!

Healthy Zucchini Muffins – Dietary Swaps

  • Vegan Zucchini Muffins – I’d recommend making my Vegan Zucchini Bread, but baking it as muffins instead. Otherwise, if you’d like to play around with this specific muffin recipe, you can use maple syrup for honey and flaxeggs for the regular eggs. I haven’t tried this yet myself, but one reader reported successfully using 1 flaxegg (combine 1 tablespoon flaxseed meal and 3 tablespoons water; let gel for 5 minutes) and 1 baking soda egg (combine 1 teaspoon of baking soda with 1 tablespoon of white or apple cider vinegar).
  • Gluten Free Zucchini Muffins. In place of the white whole wheat flour, use a GF 1:1 baking flour like this one.
  • Oatmeal Zucchini Muffins. I haven’t tried adding oatmeal, but several readers reported doing this with success. Feel free to read through the comments. There are lots of tips and suggestions there for ways you can make this zucchini muffin recipe your own.

Grating Zucchini for Muffins

A few important tips to make your Healthy Zucchini Muffins as tasty and nutritious as possible:

  • You don’t need to peel your zucchini to make zucchini muffins. The peel contains a number of nutrients and is very thin and mild. You won’t be able to taste it. Instead of peeling, simply wash your zucchini, trim the ends, then grate away.
  • For grating zucchini, I like to use a box grater like this one or a coarse plane-style grater like this one.
  • Squeeze. Blot. Repeat. A very important step to any baked zucchini recipe is to squeeze as much liquid from the grated zucchini as possible. Pile your grated zucchini onto a pile of paper towels. Press out as much water as you can, then repeat until most of the moisture is gone.

Storing Healthy Zucchini Muffins

These healthy zucchini muffins are exceptionally freezer friendly. If you make a big batch and stash a few extras in your freezer, you’ll have an on-the-go breakfast or an emergency, day-changing treat ready any time you need it!

For storage tips, check out my post about How to Store Muffins and Other Quick Breads.

Healthy Zucchini Muffin with chocolate chips - a bite taken out of the muffin

Let’s keep on taking a bite out of summer with these Healthy Zucchini Muffins!

More Freezer Friendly Healthy Muffin Recipes

Recommended Tools to Make Healthy Zucchini Muffins

muffin pan full of Chocolate Chip Banana Healthy Zucchini Muffins

Healthy Zucchini Muffins with Chocolate Chips

4.92 from 106 votes
Moist and fluffy healthy Zucchini Muffins. Whole wheat, naturally sweetened, and perfect for adding chocolate chips. Freezer friendly and utterly delicious!

Prep: 15 mins
Cook: 20 mins
Total: 35 mins

Servings: 12 muffins

Ingredients
  

  • 2 cups shredded, unpeeled zucchini (about 1 small/medium zucchini)
  • 1/2 cup mashed ripe banana about 1 medium/large or 4 ounces
  • 1/4 cup coconut oil melted and cooled, very light olive oil, or canola oil
  • 1/4 cup honey
  • 1/4 cup brown sugar light or dark
  • 1 teaspoon pure vanilla extract
  • 2 large eggs at room temperature
  • 1 teaspoon ground cinnamon
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon baking powder I recommend aluminum free
  • 1/2 teaspoon kosher salt
  • 2 cups white whole wheat flour
  • 1/3 cup semi-sweet chocolate chips mini or regular (I used mini)

Instructions
 

  • Preheat the oven to 375 degrees F. Lightly grease a standard 12-cup muffin tin or line with paper liners.
  • Grate the zucchini, then throughly squeeze it with a paper towel to remove as much excess water as possible. Repeat as needed. If you have not already, melt the coconut oil and let come to room temperature
  • In the bowl of a standing mixer or a large mixing bowl, beat together the banana, honey, brown sugar, coconut oil, and vanilla extract until smooth. Add the eggs (make sure they are room temperature or the coconut oil may resolidify), then beat again until combined.
  • Sprinkle the cinnamon, baking soda, baking powder, and salt over the top of the batter, then mix to combine. Sprinkle in the flour, then mix on low speed, just until the flour disappears. By hand, fold in the zucchini and chocolate chips.
  • Scoop the batter into the prepared muffin cups, filling them 3/4 of the way. Bake for 20-25 minutes, until a toothpick inserted in the center comes out clean. Remove the muffins from the oven and place the pan on a wire rack. Let cool for 5 minutes in the pan, then carefully lift the muffins out of the pan and place them on a wire rack to cool completely (this will keep the muffins from becoming soggy).

Notes

  • Store muffins at room temperature according to my guide to store muffins, or individually wrap and freeze for up to 3 months. Let thaw overnight in the refrigerator (or if you are in a hurry, unwrap and microwave gently on reduced heat until warm).
  • For tips to make the muffins vegan or gluten free, see blog post above.
  • For even more suggestions for how to vary up the recipe (adding oatmeal, using flaxeggs, etc.) skim the comments. There are many helpful suggestions from those who have reported making (and loving!) these muffins.

Nutrition

Serving: 1muffinCalories: 201kcalCarbohydrates: 31gProtein: 5gFat: 8gSaturated Fat: 5gPotassium: 225mgFiber: 3gSugar: 14g

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Erin Clarke

Hi, I'm Erin Clarke, and I'm fearlessly dedicated to making healthy food that's affordable, easy-to-make, and best of all DELISH. I'm the author and recipe developer here at wellplated.com and of The Well Plated Cookbook. I adore both sweets and veggies, and I am on a mission to save you time and dishes. WELCOME!

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308 Comments

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  1. These were very good and exactly the type of recipe I needed today. I used blueberries instead of chocolate chips and canola for the oil. My toddler likes them too. Not out of this world good, but very good and filling. Mine baked for 20 minutes5 stars

  2. These are hands down the best zucchini muffins I’ve ever tried. They are a family favourite and super quick and easy to make. I leave the sugar out completely to be honest but my kids and husband are obsessed. I always make a double batch too! They freeze wonderfully in an air tight container and taste so good no one even thinks about the veg!5 stars

    1. Hi Esther, that makes me so happy to hear! So glad you enjoyed the recipe! Thank you for this kind review!

  3. I just finished taste testing my first batch of these. They are so good. Thank you for this recipe!5 stars

  4. These muffins are really good, especially for how healthy they are! I still have shredded zucchini in my freezer from last summer that I had forgotten about and had an extremely ripe banana, which meant this was the perfect recipe to stumble across. I do not have white whole wheat flour but used regular whole wheat flour so head’s up they are a little more dense than your average muffins. Next time I will check the muffins sooner than 20 minutes, because they were done at 20 and I wish I had baked them a minute or two less. But overall very delicious and my husband loved them too!5 stars

    1. Hi Jody! You are correct, using whole wheat flour will result in a more dense muffin. Glad it worked out for you and that you enjoyed them! Thank you for this kind review!

  5. I haven’t tried this yet, but it looks delicious and all the reviews and comments have me convinced I need to make this. I couldn’t find white whole wheat flour at the store, would a regular all purpose flour be ok to use?

    1. Hi Christina! You can also all-purpose flour for the whole wheat. I hope you enjoy the muffins!

  6. Our garden is overflowing with zucchini so I’m frantically looking for ways to use it. After making 2 loaves of traditional zucchini bread, and it being devoured, I was so happy to find this healthier option! I used Great Value gluten free flour (works well as a 1:1 substitute) and vegetable oil instead of coconut since that was all I had on hand. I keep bananas frozen for smoothies and just put one directly in the mixer since they thaw so quickly. They turned out awesome! My husband and mom said I could feel free to make them anytime for them! Thanks for this recipe!5 stars

  7. This looks delicious! Is the shredded zucchini measured before or after you squeeze out the liquid from it? Thank you.

  8. I made this muffins today, I was looking for a healthy treat to indulge my family. They turned amazing! I used 1 cup whole wheat flour and 1 cup of spelt flour. Instead of brown sugar I used 1/4 cup of date sugar and I used olive oil instead of the coconut oil .
    Before baking them I drizzled them with date syrup. Absolutely delicious! Thanks for the recipe!5 stars

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