Zucchini Muffins with Chocolate Chips
Super moist, healthy, and packed full of flavor, these healthy zucchini muffins with chocolate chips are my favorite way to enjoy one of the summer’s best vegetables!

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Muffins can be so many things…super indulgent (almost like a cupcake) like my Apple Streusel Muffins, or packed full of nutrients for a super healthy snack like my Blueberry Protein Muffins. My Zucchini Muffins with Chocolate Chips meet somewhere in the middle. I would say they lean closer to the healthier side, but still have a yummy indulgent flavor!
Packing shredded zucchini into baked goods is such a great way to add nutrients and lots of moisture! Its flavor is virtually undetectable for picky eaters. With the many benefits it provides, zucchini is a great addition to use in baking and the yummiest way to eat your veggies! You’ll LOVE my Double Chocolate Zucchini Bread too!
This recipe makes 12 standard size muffins and would be perfect served for breakfast or brunch along with something like my Biscuits and Gravy or Easy Belgian Waffles.
Why You’ll Love this Recipe
- It’s made with healthier ingredients, but still tastes indulgent! Using mashed banana instead of sugar and incorporating wheat flour makes these muffins a healthier option, but yields a delicious treat!
- They freeze really well – use up all that summer zucchini and save muffins in the freezer to enjoy for several months!
- They’re so easy to make! No mixer required – you can mix up the batter quickly by hand.
How to Make Healthy Zucchini Muffins with Chocolate Chips
Ingredients

While this recipe has several ingredients, they are most likely things you’ll already have in your pantry. A few things that make this recipe healthier:
- Zucchini – Grate the zucchini with a cheese grater or your shredding attachment on your food processor. No need to drain your zucchini! This adds amazing moisture to the muffins!
- Banana – Ripe bananas here! The more ripe, the more sweetness it will add. You may even want to experiment with cutting back on some of the honey if you use super ripe bananas. This could cut back even more on the sugar in your recipe!
- Greek Yogurt – This makes the muffins extra tender and moist, as well as adding protein.
- Whole Wheat Flour – Using whole grains ensures that you’re getting all the health benefits from the grain, including fiber-rich bran. I love Baking with Whole Grains because they add extra nutrition, flavor and make me feel fuller longer. Feel free to adjust the amount of whole wheat flour in this recipe…you could increase or decrease it according to what you like!
- Cinnamon & Nutmeg – These spices add a cozy flavor to the muffins…almost like they’re transitioning you from Summer to Fall.
Directions
- Add the dry ingredients to a large bowl.
- Stir them together until combined.
- In a separate bowl, use a wire whisk to combine the wet ingredients.
- Add the wet ingredients to the dry ingredients and stir until combined. The batter will be thick.
- Add the mini chocolate chips and shredded zucchini.
- Stir until all combined. The batter will be wetter with the addition of the zucchini.
- Fill each well of a standard muffin tin sprayed with nonstick spray. Fill about 2/3 full and bake. Bake at 400°F for 5 minutes to help give the muffins a zap of heat to rise. Then reduce the oven temperature to 375°F and bake an additional 18-22 minutes.
- Allow the muffins to rest in the pan about 5 minutes before removing to a wire cooling rack.


Variations
- Add in chopped nuts, blueberries, apple chunks, or raisins. Feel free to play around with the flavors and textures here and make it exactly how you like! Make sure you read about the important ingredients in the beginning of this post (scroll back up).
- Make it gluten free by replacing the wheat and white flours with a 1:1 gluten free flour.
- Use a different whole grain flour like spelt or rye – whatever you have on hand or prefer. You can also play around with the amount of whole grain flour in this recipe like using half and half or 100% whole wheat flour. Just keep in mind, the more whole grains you use, the more dense the muffins will be.
Storing
Store these healthy zucchini muffins in an airtight container on the counter for up to three days. Extend the shelf life by putting them in the refrigerator for up to five days. You can also freeze them in an airtight container for up to 3 months – if you’ve got lots of zucchini to use up, this is a great option!

More muffin recipes
If you love my zucchini muffins with chocolate chips, you’ll love these muffins too:
Pumpkin Discard Muffins with Maple Icing
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Healthy Zucchini Muffins with Chocolate Chips
Ingredients
- 1 ¼ cup all-purpose flour *
- ¾ cup whole wheat flour *
- ½ teaspoon fine salt
- ½ teaspoon baking soda
- 1 teaspoon baking powder
- 1 ½ teaspoon ground cinnamon
- ¼ teaspoon nutmeg
- ⅓ cup mini chocolate chips
- 2 large eggs
- ¼ cup greek yogurt
- ¼ cup coconut oil, melted (can use vegetable or canola oil)
- ⅓ cup honey
- 1 teaspoon vanilla extract
- ½ cup mashed, ripe banana (about 1 medium)
- 2 cups shredded zucchini (about 1 medium)
Instructions
- Preheat oven to 400°F. Grease a 12-cup muffin tin or line with muffin liners. Set aside.
- In a large mixing bowl, whisk together the all-purpose flour, wheat flour, salt, baking soda, baking powder, cinnamon, and nutmeg. Add the mini chocolate chips and toss to combine with the flour mixture. Set aside.
- In a separate bowl, whisk together the eggs, Greek yogurt, oil, honey, vanilla, and mashed banana.
- Add the wet ingredients to the dry ingredients and stir to combine.
- Add the shredded zucchini (no need to drain it). Stir to combine.
- Spoon muffin batter into each muffin cup, filling 2/3 full.
- Bake for 5 minutes. Reduce oven temperature to 375°F and bake an additional 18-22 minutes, until a toothpick inserted into the center comes out clean. Remove from oven and place pan on a wire cooling rack. Allow to cool for 5 minutes before removing muffins from pan. Continue cooling muffins on rack. Serve and enjoy!
Notes
- See this recipe post for more detailed pictures and step by step instructions.