These incredibly moist and delicious Banana Chocolate Chip Zucchini Muffins are made healthier with whole wheat flour and applesauce! Perfectly sweet and packed with flavor, they are a great way to use up summer zucchini and make an ideal back-to-school snack. They also freeze super well, making them a perfect grab-and-go treat that kids absolutely love!

Ultra Moist & Flavorful Zucchini Muffins
Any time I can hide my vegetables in chocolate, count me in.
I can’t honestly say that I eat a lot of zucchini that’s not baked into something (take this apple zucchini bread and chocolate zucchini cake for example), but I sure do love it paired with banana and chocolate. I like to think it makes these banana chocolate chip zucchini muffins healthy enough to indulge in on a regular basis!
I first made these muffins last summer when I was overloaded with zucchini. Now, I look forward to zucchini season just so I can stock the freezer with them! It’s also kind of nice that zucchini season and back-to-school season happen at the same time, because these muffins make such an awesome school snack or breakfast.
These muffins have tons of good healthy stuff going on. Zucchini, banana, whole wheat flour, unsweetened applesauce… so I didn’t feel too bad adding the chocolate in there, too 😉
This recipe is tied for first place with my other favorite banana chocolate chip muffins. They are so moist, the recipe makes a bunch and they freeze perfectly.

Ingredients for Banana Chocolate Chip Zucchini Muffins
- Overripe bananas: The browner, the better! If you keep a stash in the freezer like I do, just let them thaw before using.
- Zucchini: You’ll want to grate this. No need to peel it unless you really want to!
- Brown sugar: Either light or dark brown sugar will work just fine here.
- Applesauce: Make sure it’s unsweetened, or your muffins will be too sweet.
- Canola oil: Any neutral-flavored oil like vegetable or melted coconut oil will also work.
- Flour: I use a mix of all-purpose and whole wheat for something a little healthier.
- Chocolate chips: Totally optional, but are they really? Mini or regular-sized both work great.
Quick Tips for Flawless Banana Zucchini Muffins
- I sprinkle a few extra chocolate chips on top of each muffin right before they go in the oven. It makes them look extra pretty and gives you that nice melty chocolate on top!
- Make sure to really squeeze the water out of the shredded zucchini. I usually wrap it in a cheesecloth or a clean dish towel and twist until no more liquid comes out. This prevents the muffins from getting soggy.
- When it comes to mixing the wet and dry ingredients, I just stir until I don’t see any more flour streaks. It’s better to have a few lumps than to overmix and end up with tough muffins.
- I like to use an ice cream scoop to fill the muffin liners. It’s less messy and helps make sure they’re all the same size so they bake evenly.

How to Store Banana Chocolate Chip Zucchini Muffins
These muffins can be stored in an airtight container at room temperature for up to 3 days. If you’re like me and LOVE that fresh-out-of-the-oven taste, just pop them in the microwave for about 15 seconds when ready to eat.
Banana Chocolate Chip Zucchini Muffins FAQs
Not at all! The zucchini adds incredible moisture and texture, making the muffins super soft and tender, but you can’t taste it. It’s a fantastic way to sneak in some extra veggies, and even picky eaters won’t be able to tell it’s there.
Yes. This recipe makes a really large batch, because I am allllll about my freezer. They freeze perfectly for at least a few months, and you can just give them a quick zap in the microwave and they’re as good as fresh. With school around the corner (and my baby going into kindergarten!), I’m sure I’ll be stocking up for easy school snacks.
Yes, you can easily make this recipe gluten-free. Simply substitute the all-purpose flour with a 1:1 gluten-free baking flour blend. Make sure the blend contains xanthan gum for the best structure. For more gluten-free goodness, take a look at my gluten-free ice cream sandwiches!
If you loved these muffins, please leave a star rating and comment below to let us know! We love hearing from you!
Banana Chocolate Chip Zucchini Muffins

Ingredients
- 3 overripe bananas, (I put mine in the freezer and let them thaw before using)
- 2 ½ cups shredded zucchini
- 2 tsp vanilla
- 5 large eggs
- 1 ½ cups brown sugar
- 1 cup unsweetened applesauce
- ½ cup canola oil, or oil of choice
- 2 cups all-purpose flour
- 2 cups whole wheat flour
- ½ tsp salt
- 1 tsp baking powder
- 2 tsp baking soda
- 3 tsp cinnamon
- 1 ½ cups chocolate chips, optional
Instructions
- Preheat oven to 325°F (you can do 350℉ if using light colored pans) and line 3 12-cup muffin pans with paper liners.
- In a large bowl, mash bananas with a whisk. Add zucchini, vanilla, eggs, brown sugar, applesauce and oil and whisk well to combine.
- Add flours, salt, baking powder, baking soda and cinnamon all at once and whisk until just combined (you want them evenly distributed, but don't overmix). Stir in chocolate chips if desired.
- Spoon batter into paper liners and bake at 325℉ for 20-22 minutes, until a toothpick comes out clean.
- Let rest 10 minutes before removing from the pan to cool completely.
Video
Notes
- Make sure to really squeeze the water out of the shredded zucchini. I usually wrap it in a cheesecloth or a clean dish towel and twist until no more liquid comes out. This prevents the muffins from getting soggy.
- When it comes to mixing the wet and dry ingredients, I just stir until I don’t see any more flour streaks. It’s better to have a few lumps than to overmix and end up with tough muffins.
- I like to use an ice cream scoop to fill the muffin liners. It’s less messy and helps make sure they’re all the same size so they bake evenly.
- I sprinkle a few extra chocolate chips on top of each muffin right before they go in the oven. It makes them look extra pretty and gives you that nice melty chocolate on top!
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.
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linda says
I have made these muffins several times using fresh grated zucchini and they have turned out great. I would like to try making them from frozen grated zucchini. When you thaw your frozen zucchini. Do you drain off excess liquid?
If so after draining it doesn’t measure as much, about !/2 cup less but Still looks very moist. Has anyone tried making these muffins with frozen zucchini?
Ashley Fehr says
I haven’t tried with frozen zucchini but I would probably drain some liquid, but not squeeze totally dry. I’d love to hear how it works!
Sarah @Whole and Heavenly Oven says
I’m all for sneaking healthy stuff into my muffins!! I’ll bet these beauties are INSANELY moist thanks to the banana and zucchini!
Ashley Fehr says
Yes, one of my favorites! Thanks Sarah!
Gayle @ Pumpkin 'N Spice says
I’n right there with you…I don’t eat a whole lot of zucchini that’s not baked into something (though i am getting better about zoodles) but I do love the veggie. These muffins look perfect for breakfast or snack. i love the banana and chocolate chip combo! Sounds so good and a great way to use up that zucchini!
Ashley Fehr says
My plant is getting bigger everyday so I’m hoping for a lot! I see a lot of baking in my future 😉
Mary Frances says
I just used up all my ripe bananas for a banana bread, but I’m excited to try this soon! I’ve always loved mixing zucchini in there but haven’t done it in so long. Thank you for sharing!
Ashley Fehr says
Thanks Mary!
Nancy Orr says
I need nutrition info and can you make them without salt
Ashley Fehr says
You can input the information into this site: https://www.myfitnesspal.com/recipe/calculator. Yes, I imagine they can be made without salt.
Becky says
My son is allergic to apples and is gluten intolerant. I used 4 cups of King Arthur’s gluten free flour, skipped the apple sauce, and threw in an extra banana. They came out perfect following all the other portions, temperatures, and times in the recipe. Delicious!
Diane says
I took these out of the oven 20 minutes ago and three are already gone – taken by the same person! Moist and delicious! A recipe to keep! Thank you for sharing.
Ashley says
I’m so glad Diane! Thanks for leaving a comment! This is one of my favorite muffin recipes 🙂
Michelle @ A Dish of Daily Life says
This is some serious deliciousness here! Your muffins look so good! I’m definitely pinning these…I can’t wait to try them! If you have a free moment, I would love for you to link them up with us at Foodie Fridays…we go live at 9 pm tonight. Happy Friday!
Krista @ Joyful Healthy Eats says
Sounds like the perfect way to start the morning to me… fruits vegetables and chocolate! YUM!
Ashley says
You’ve gotta have chocolate, right?!
Emily @ It Bakes Me Happy says
Oh goodness Ashley these muffins look delicious, I love the zucchini with banana, I think I need to try this soon, my kids love banana bread!
Ashley says
I love banana bread too! It’s nothing original, but it’s one of my favorite muffin recipes!
Medha @ Whisk & Shout says
These look wonderful and I have a ton of overripe bananas waiting to be baked into something!
Ashley says
Thanks Medha! We love them!
Jess @ On Sugar Mountain says
I love these muffins that are full of secret veggies but also plenty of chocolate chips and banana! What a perfect Fall breakfast! 😀
Shashi @ runninsrilankan says
Yum – bananas, zucchini and chocolate never looked so good!!
Shashi @ runninsrilankan says
Yum – bananas, zucchini and chocolate never looked so good!
Ashley says
Thanks Shashi!
Thalia @ butter and brioche says
Nothing beats a good home baked banana and chocolate chip muffin, but I never would have thought to add zucchini in before! Curious to know what they taste like with the added zucchini, will have to recreate the recipe and report back!
Ashley says
Definitely! You actually can’t taste it at all. I’m not a huge veggie lover, so they have to be pretty well hidden 🙂
Annie @Maebells says
These are beautiful! And I love how much good stuff you crammed into these muffins! Delish!
Ashley says
Haha, I try! It makes me feel better about everything else I eat! Thanks 🙂
Matt Robinson says
These look amazing, and my boys would love them without a doubt. Love that they’re made healthier too!
Ashley says
Thanks Matt! I’ve still got a pail full in the freezer and I love them for lunches!