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

4.91 from 132 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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372 Comments

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  1. WOW! Just made these as a snack for my sometimes picky almost 2 year old. Well, he wouldn’t share! He devoured 2 large muffins all on his own! – I used gluten free flour to make mine and kept and eye on the timer, they are perfect! Not too sweet, not too dense! Thanks for this awesome recipe!5 stars

  2. These are awesome! Both my 1 year old and I loved them. Will be making a double batch next time. I made them vegan by using flax eggs and date syrup to replace normal eggs and honey. I also used chocolate nibs instead of chocolate chips. Thanks so much for the amazing, easy recipe5 stars

  3. I made literally dozens and dozens of these to share during 2020, when we couldn’t actually see anyone, and our garden was producing an over-abundance of zucchini. Most people weren’t welcoming more zucchini, but were thrilled with the muffins. I have used both regular whole wheat and white. White is a finer texture, regular slightly more “rustic.” We loved both! It’s now one of my most favorite ways to use zucchini. Thanks!5 stars

  4. Lovely recipe, Only thing I changed was I added 2/3 a cup of chopped pecans: canola oil works nicely and you don’t have to worry about the eggs coming to room temp as much5 stars

  5. I followed the recipe to a T but the muffin batter came out extremely dry (like very shaggy bread dough). I ended up adding extra oat milk just to get it back to a muffin-like batter. Did anyone else have this issue?

    1. I’m sorry you to hear had trouble with the recipe. I know it’s frustrating to try a new recipe and not have it turn out. I (and many other readers) have enjoyed them, so I really wish they would’ve been a hit for you too! It’s hard to say what went wrong without being in the kitchen with you.

  6. Great recipe!
    I changed it up a bit to make it GF/egg free/refined sugar free and used GF flour, chia eggs and a mixture of coconut sugar and erythritol instead of brown sugar. Can’t speak to how they compare to the original recipe, but just ate two still warm from the oven and they were delish.5 stars

  7. Hello! I was looking for a healthy recipe that I could do from items in my pantry! Yours popped up and I only had to substitute the flour! (I used almond instead!) man oh man are they delish!!! Im going to try your oatmeal ones next! Cant wait to try more yummy recipes! Thank you so much!5 stars

  8. Just made these delicious zucchini muffins. They came out perfect and so delicious. I’ll be making these again, for sure.5 stars

  9. These turned out AMAZING! Thank you for sharing this recipe with us. I will definitely be using throughout the summer!5 stars

  10. These are so delicious! Next time I want to add walnuts because I appreciate a good crunch. It’s my first time using coconut sugar and coconut oil, so I wasn’t sure how they would be as a substitution. But they turned out great! I did half AP half whole wheat flour. Shared them with coworkers, and they all wanted the recipe. Luckily I have a dozen still in my freezer because I doubled the recipe.5 stars

    1. Hi Sharon, I haven’t tested this out myself but you might be able to use unsweetened applesauce. If you decide to experiment, let me know how it goes!

  11. Taste and texture were not sacraficed for healthiness! I love these muffins, espcially warmed in the microwave!5 stars

  12. These healthy and easy to make muffins were a crowd pleaser! They were the perfect consistency without being too dry. Next time I make them I will definitely make extra to store in the freezer. They’re a great use of fresh, summer zucchini!5 stars

  13. This recipe looks awesome. Do you know whether it’s possible to puree the zucchini, rather than grate it? I’m trying a figure out how to really keep it undetected for my super picky kids. Would love your insight. Thank you!

    1. Hi! I haven’t tried to puree it before adding it to the muffins. If you decide to experiment, let me know how it goes!

  14. I literally make these constantly and do not get sick of them 😂
    They are sooo good. I do variations sometimes: chocolate nibs instead of choc chips, flax egg instead of prepped eggs, buckwheat flour instead of whole meal flour, and rice syrup instead of honey. You just can’t seem to go wrong with these! Such a great guilt free snack. My daughter and I love them. Thanks so much for the recipe5 stars

  15. Delicious! Added a little extra chocolate chips. My teen who was skeptical bc of the zucchini loved them too! Would definitely make again.5 stars

  16. Delicious! Added a little extra chocolate chips bc only had regular size, I think the mini would be better. My teen who was skeptical bc of the zucchini loved them too! Would definitely make again.5 stars

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