Healthy Zucchini Muffins are made with honey, whole wheat flour, banana, and chocolate chips. Moist, fluffy, and kids love them too! This healthy zucchini muffin recipe makes the perfect lunch box treat.

After ransacking my entire freezer on Tuesday afternoon in a desperate search find the last, lonely Chocolate Chip Zucchini Muffin, I decided that, despite the fact that I’ve been bombarding you with recipes involving zucchini and overly ripe bananas, I couldn’t wait one more day to share this recipe. What if you urgently needed a healthy, moist, and chocolate-studded treat like these healthy zucchini muffins too?

muffin pan full of Chocolate Chip Banana Healthy Zucchini Muffins

I reasoned that I best share this healthy zucchini muffins recipe immediately, before you lived one more day without them in your life. Does that sound too dramatic? Can a zucchini muffin recipe with chocolate chips really be life changing?

Day-Changing Healthy Zucchini Muffins

overhead image of Healthy Zucchini Muffins studded with chocolate chips

Perhaps not life changing, but I can attest from personal experience of the most painful variety, that these moist, fluffy, chocolate zucchini muffins are at the very least day changing, which after the morning I had, was desperately needed.

In the span of three hours, I managed to:

  • Reactivate an old running injury, which necessitated that I walk around my kitchen with an ice pack strapped to my hip.
  • Spring a leak in said ice pack, which dripped all over my shorts and looked (and felt) suspiciously as if I’d wet my pants.
  • Dump a blueberry pie smoothie down my shirt.
  • Knock a container of sprinkles off the top shelf. The container burst open and tiny colored balls went EVERYWHERE.
  • Dump sparkling sugar all over the top of my perfect peach pie. The sugar lid fell off mid-shake and turned my intended sprinkle into an avalanche.

What I should have done was climb back into bed, step out the other side, and promptly devour a chocolate chip studded zucchini muffin.

Chocolate Chip Banana Zucchini Muffin with a pan of muffins behind it

What I actually did was spill milk all over my counter (truly). THEN, I ate a chocolate zucchini muffin.

At least I still got the chocolaty healthy zucchini muffin the in end.

After posting this recipe for Chocolate Chip Paleo Zucchini Bread, I received a few requests for a “regular” version of the recipe, made with wheat flour instead of coconut flour. While I still adore coconut flour and recommend trying it, I recognize that it’s not for everyone, and even if it is, can a girl ever have too many tasty, healthy zucchini bread or muffin recipes at her disposal? I think not.

2 speckled ripe bananas and 3 whole zucchini

Today’s healthy zucchini muffins are hands-down one of my favorite muffin recipes I’ve ever baked. They are naturally sweetened with honey, and despite the fact that they contain no butter, they are marvelously moist, thanks to the addition of mashed banana and zucchini. (If you want to make a loaf instead of muffins, check out this Zucchini Banana Bread!)

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

Healthy Zucchini Muffins Mix-Ins

I’ve baked these healthy zucchini muffins twice now, the first time with mini chocolate chips (my favorite) and the second with walnuts (Ben’s favorite). I think they’d also be fantastic with fresh or frozen blueberries and dried cranberries too. I’d love for you to choose your own healthy zucchini muffin adventure, then let me know how they come out for you!

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

As I can attest, these healthy zucchini muffins are also very 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.

More Freezer Friendly Healthy Muffin Recipes:

Tools I used to make the healthy zucchini muffins recipe:

muffin pan full of Chocolate Chip Banana Healthy Zucchini Muffins
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Healthy Zucchini Muffins with Chocolate Chips

Yield: 12 muffins
Prep Time:
15 mins
Cook Time:
20 mins
Total Time:
35 mins
Chocolate Chip Healthy Zucchini Muffins. Made with honey, whole wheat flour, and banana. Moist, fluffy, and kids love them too!


  • 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)


  1. Preheat the oven to 375 degrees F. Lightly grease a standard 12-cup muffin tin or line with paper liners.
  2. 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
  3. 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.
  4. 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.
  5. 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).

Recipe Notes

Store muffins at room temperature according to my guide to store muffins, or individually wrap and freeze for up to 2 months. Let thaw overnight in the refrigerator (or if you are in a hurry, unwrap and microwave gently on reduced heat until warm).
Course: Breakfast
Cuisine: American
Keyword: Healthy Muffin Recipe, Healthy Zucchini Muffins with Chocolate Chips

Nutrition Information

Amount per serving (1 muffin) — Calories: 200, Fat: 8g, Saturated Fat: 6g, Cholesterol: 31mg, Sodium: 116mg, Carbohydrates: 30g, Fiber: 19g

Did you try this recipe? I want to see! Follow Well Plated on Instagram, snap a photo, and tag it #wellplated. I love to know what you are making!

titled photo collage - healthy zucchini muffins with chocolate chips