Chocolate Zucchini Muffins are packed with zucchini and double the chocolate for a muffin that tastes like dessert, yet is healthy enough for breakfast.

Chocolate Zucchini Muffin with bite out of it next to chocolate chips and cocoa powder.

While nothing compares to my mom's zucchini bread and I could go to town snacking on air fryer zucchini fries, I can never resist a chocolate zucchini muffin. And these double chocolate zucchini muffins are my kid's all-time favorite zucchini recipe.

Why You Will Love These Muffins

Good For You. Instead of being loaded with refined flour and sugars, this recipe for chocolate zucchini muffins is made with whole grains, sweetened with honey, and lower in fat. But don't worry, even those these muffins are healthy, they taste sinful.
Amazing Texture. Even though these Chocolate Zucchini Muffins are made with whole wheat flour, they bake up light and tender and stay perfectly moist thanks to the addition of zucchini and applesauce.
Double the Chocolate. These zucchini muffins don't skimp on the chocolate. The batter is made with rich cocoa powder and the muffins are studded with chocolate chips.
Filled with Vegetables. Just like Healthy Carrot Cake Muffins and Healthy Pumpkin Muffins, no one will complain about eating their veggies when they bite into one of these Healthy Zucchini Muffins. This healthy muffin recipe makes eating your vegetables feel decadent!

Notes on Ingredients

Ingredients for zucchini muffins labeled on counter.

Whole White Wheat Flour: Instead of all-purpose flour, I opt to use whole white wheat flour, which is 100% whole grain, yet bakes up just as light as all-purpose flour.
Chocolate Chips: Chocolate Chips can be omitted to keep these muffins 100% free from refined sugars, but I recommend adding them for a burst of fudgy deliciousness. I love to use mini chocolate chips but regular chocolate chips work as well.
Applesauce: Applesauce is used to cut back on the amount of oil needed, while still keeping these muffins light and tender. It also helps to naturally sweeten the muffins.
Oil: Use either canola oil, melted and cooled butter, or melted and cooled coconut oil.
Honey Instead of using granulated sugars, these muffins are sweetened with honey.
Milk: To keep the muffins light and fluffy, milk is needed. You can use dairy or non-dairy milk based on your preference.

How To Make Chocolate Zucchini Muffins

Step One: Prepare Zucchini. It is important to remove the excess water from the zucchini, just as you would when making Zucchini Bread. This will keep the muffins from becoming dense and mushy.

I find that the best way to remove the excess liquid from grated zucchini is to place it into a piece of cheesecloth and give it a good squeeze over the sink.

Side by side photo showing grating zucchini.

Step Two. 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.

Side by side bowl showing dry ingredients before and after sifting.

Step Three: Combine 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 overmixing the batter, which can result in dense muffins.

Side by side bowl before and after mixing together the wt ingredients.

Step Three: Fold Together. When working with muffins or quickbread 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.

Side by side photo showing muffin batter before and after adding zucchini and chocolate chips.

Step Four: 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 is the least messy way to distribute the batter into the muffin tin.

Chocolate Zucchini Muffin Batter in muffin tip topped with chocolate chips.

Step Five: Bake. Bake the zucchini muffins 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 your muffins don't overbake.

Healthy Zucchini Muffins on wire rack cooling.

Storing Zucchini Muffins

Because these zucchini muffins are loaded with zucchini and are whole grains, they are best stored in the refrigerator if stored longer than 24 hours.

Once cooled, pop the muffins into an airtight container or freezer-safe bag and place the muffins in the refrigerator for up to 5 days. Alternatively, you can freeze the muffins for up to 3 months. Just pop them into a freezer-safe storage container bag once fully cooled and place them into the freezer.

Recipe Modifications

Gluten-Free Zucchini Muffins: Replace the whole white wheat flour with an equal amount of 1:1 gluten-free all-purpose flour blend. I have done this many times with success.
Dairy-Free Zucchini Muffins: Be sure you use dairy-free chocolate chips and use your favorite non-dairy milk in place of milk for this recipe. I tend to use unsweetened plain almond milk when making these muffins dairy-free. Canned coconut milk is a great addition if using melted coconut oil, just be warned it will result in a slight "coconut" flavor. But chocolate + coconut is a great match!
Egg-Free Zucchini Muffins: A flax egg substitute can be made to keep these muffins egg-free with great success. Simply mix 1 tablespoon of ground flaxseed with 2 tablespoons of water and let sit for 5 minutes before adding to the muffin batter.
Vegan Zucchini Muffins: With SEVERAL changes, these muffins can be made vegan-friendly. I have done this many times and the results are spectacular. Use a flax egg to replace the egg, use maple syrup instead of honey, and use non-dairy chocolate chips, and non-dairy milk.

More Recipes Using Zucchini

If you enjoyed these Chocolate Zucchini Muffins, I would love for you to leave a comment and review below.