This post may contain affiliate links. Please see our disclosure policy.
These Chocolate Zucchini Muffins are EVERYTHING you crave in a good muffin. Made with whole grains, sweetened with honey, and featuring double the chocolate, this recipe delivers a perfectly moist muffin that tastes decadent, yet is packed with wholesome ingredients.
Have an abundance of zucchini? After enjoying these Double Chocolate Zucchini Muffins, try out my recipes for Pineapple Zucchini Bread, Grilled Vegetable Kabobs, and Air Fryer Zucchini Fries.

Double the Chocolate Double the Deliciousness

While I am obsessed with my grilled zucchini salad and I love sauteed zucchini, getting my kids excited to eat zucchini is another story.
However, they have no trouble devouring zucchini in the form of these Chocolate Zucchini Muffins.
With a rich chocolate batter and melty chocolate chips, these Double Chocolate Zucchini Muffins taste decadent, yet are loaded with veggies and whole grains. Not to mention, they use a lot less oil and the batter is naturally sweetened, making these muffins a wholesome treat!
The perfect zucchini recipe for kids-and adults too! 😉
Happy Cooking! xo Kristen
Notes on Ingredients
You will find the full list of ingredients, along with quantities in the recipe card. Below is a quick glance at what you need and tips to help you make the right selection.

- Zucchini: This calls for 1 cup of shredded zucchini, which is equivalent to 1 large zucchini or 2-3 smaller zucchini.
- Flour: I recommend using whole white wheat flour, as it is still 100% whole grain, yet bakes up lighter and fluffier than traditional whole wheat flour. Feel free to replace with a 1:1 gluten-free all-purpose flour blend to keep the muffins gluten-free.
- Double the Chocolate: Use both unsweetened cocoa powder and chocolate chips (milk chocolate, dark chocolate, or semi-sweet) to give these muffins their irresistible chocolate flavor.
- Oil + Applesauce: Using a combination of unsweetened applesauce and oil (canola oil or melted and cooled coconut oil), ensures these muffins are light and tender, while drastically cutting down on the amount of fat added to the recipe.
- Milk: Use your favorite milk or unsweetened non-dairy milk to help thin the batter.
- Sweetener: Opt for honey or pure maple syrup, which sweeten the muffins naturally and add additional moisture to the batter.
How To Make Chocolate Zucchini Muffins
The following tips are provided to help you achieve perfect results. You will find the ingredient quantities and detailed instructions in the recipe card at the bottom of this post.
- Prepare Zucchini. Using a box grater or food processor fitted with a grating blade, place the zucchini in a piece of cheesecloth or clean kitchen towel and give it a good squeeze over the sink to remove the excess water from the zucchini-this is crucial to preventing your muffins from being dense and mushy.

- Sift Dry Ingredients Together. Because cocoa powder, baking powder, and baking soda are all prone to clumping together, sifting the ingredients through a fine-mesh strainer will keep your batter lump-free and each bite of your zucchini muffin delish.

- Whisk Together Wet Ingredients. It is best to whisk the honey, egg, applesauce, oil, milk, and vanilla together prior to adding them to the flour mixture. This will help prevent over mixing the batter, which can result in dense muffins.

- Fold Muffin Batter Together. When working with muffins or quick bread recipes, you don't want to overmix the ingredients. It is best to gently fold the wet ingredients into the dry ingredients until JUST combined. Once you no longer see pockets of flour, add in the prepared zucchini and chocolate chips, and using a spatula fold them into the muffin batter until JUST distributed.

- Use an Ice Cream Scoop to Fill Muffin Tin. My best tip for scooping muffin batter into a prepared muffin tin is to use an ice cream scoop. Using an ice cream scoop will keep each muffin uniform in size and keeps the mess to a minimum.

- Bake. Bake until the muffins rise, the tops are set, and a toothpick inserted into the center of the muffin comes out dry. I recommend checking on the muffins 5-10 minutes prior to the baking time listed to ensure you don't over bake the muffins.

Storage Instructions
- At Room Temperature: Because these chocolate zucchini muffins are loaded with zucchini and are whole grains, they can grow mold quickly at room temperature. It is best to let the muffins cool fully, place them in an airtight container and store at room temperature for up to 24 hours.
- Refrigerate: Once cooled, pop the muffins into an airtight container and store the zucchini muffins in the refrigerator for up to 5 days.
- Freeze: Place the cooled muffins on a cookie sheet and freeze for 30-60 minutes until solid. Once frozen solid, place them in a freezer-safe bag and store them in the freezer for up to 3 months. Defrost in the fridge overnight, or warm in the microwave for 1-2 minutes to heat before serving.
More Favorite Muffin Recipes
Did you make this recipe?
If you enjoyed this recipe, please leave a comment with a 5-star review at the bottom of the post. Thank you!
Chocolate Zucchini Muffins

Video
Ingredients
- 1 cup shredded zucchini, ~1 large or 2 medium zucchini
- 1 ½ cups whole white wheat flour, or all-purpose flour
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ¼ teaspoon salt
- ½ cup unsweetened cocoa powder
- ½ cup honey, or maple syrup
- 2 tablespoons canola oil , or melted and cooled coconut oil
- ½ cup unsweetened applesauce
- ¼ cup milk, any variety
- 1 large egg
- 1 teaspoon vanilla extract
- ½ cup chocolate chips, + more for topping if desired
Instructions
- Preheat the oven to 350℉ (175℃). Prepare a muffin pan by lining it with paper or silicone liners or greasing the muffin cups really well with butter or nonstick spray.
- Wash and dry the zucchini. Cut off the stem of the zucchini and using a box grater or food processor fitted with a grating blade, shred the zucchini. Remove excess moisture from the shredded zucchini by placing it into a piece of cheesecloth or a clean kitchen towel and squeezing it firmly over the sink. Alternatively, place the shredded zucchini into a fine-mesh colander and use your hands to really press down hard on the zucchini to remove the excess liquid. Measure out 1 cup shredded zucchini and set aside.
- Using a fine-mesh strainer, sift the 1 ½ cups whole white wheat flour, 1 teaspoon baking soda, 1 teaspoon baking powder, ¼ teaspoon salt, and ½ cup unsweetened cocoa powder over a large mixing bowl. Alternatively, whisk the ingredients together, just be sure to remove any lumps.
- In a separate smaller mixing bowl, whisk together the ½ cup honey, 2 tablespoons canola oil , ½ cup unsweetened applesauce, ¼ cup milk, 1 large egg, and 1 teaspoon vanilla extract until well combined.
- Add the wet ingredients to the dry ingredients and stir until just combined, careful to not overmix, as this can result in tough muffins.
- Fold the shredded, drained zucchini and ½ cup chocolate chipsinto the batter.
- Scoop out ¼ cup of batter into each muffin cup. Sprinkle each muffin with a couple of chocolate chips, if desired.
- Bake for 18-22 minutes, or until toothpick inserted in middle comes out dry.
- Place the baked muffins on a cooling rack and allow them to sit in the muffin tin for 5-10 minutes, before removing them from the tin. Allow the muffins to cool fully before enjoying.
Equipment
Notes
Nutrition
Nutrition information is automatically calculated, so should only be used as an approximation.













These were great. I didn't have enough zucchini to measure 1 cup so made up the difference with shredded carrots.
Oh what a great idea to use carrots! Thanks for sharing, Sharon!
By this time of year (September) you have to really hide the zucchini. These muffins are the perfect cover up - delicious, moist, with just a touch of sweetness - enough to let the rich chocolaty goodness shine through. I love the list of wholesome ingredients, almost all pantry staples. Instructions are excellent and the recipe comes together quickly. I think we actually will be sad to see zucchini season end!
LOL! Right, by September everyone is getting tired of eating zucchini if you are lucky enough to grow it. I am glad this zucchini muffin recipe is your solution 🙂 Thanks for sharing.
Very tasty. I'll bet nuts would be a great addition.