Healthy Chocolate Zucchini Muffins

Chocolate Zucchini Muffins are a moist, rich and fudgy kid-friendly breakfast, made with whole wheat, applesauce, cinnamon, semisweet chocolate chips and zucchini.

If you’ve tried Chocolate Zucchini Bread, these zucchini muffins are just as chocolatey and delicious, but made into an easy, grab-and-go Breakfast Recipe.

Healthy Chocolate Zucchini Muffins


You and your whole family will love the melty double chocolate taste of these zucchini muffins! The simple ingredients are wonderfully sweet without using too much sugar. Chocolate Zucchini muffins are a great recipe to keep in your fridge and grab on your way out the door. They can also be packed in lunches for a sweet snack during the day, or as a dessert after dinner.

No matter when you eat Zucchini Muffins you can enjoy them guilt-free. These Chocolate Zucchini Muffins have less sugar than most muffin recipes, which also reduces the calories and the carbohydrates in the muffins. This muffin recipe also calls for whole wheat flour, instead of all-purpose flour.


Have you ever wondered why zucchini recipes are so popular, especially in healthy baking? Well, there are lots of reasons. Firstly, zucchini has such a mild taste, it adds a healthy ingredient without overpowering the other flavors. So, if you have any picky eaters, you can sneak it into their diet without them ever noticing.

Zucchini is also a great source of vitamins and potassium. It’s low in calories and rich in nutrients. If you’d like to add some extra nutrients to your Healthy Zucchini Muffins leave the shredded zucchini unpeeled.

Baked goods with whole wheat have more fiber than baked goods white flour. It also contains more vitamins and magnesium. So, while these Zucchini Muffin recipe might taste like an indulgent dessert, it’s a relatively healthy recipe.



  • Add-ins: Change the chocolate chips in this recipe for milk chocolate chips, mini chocolate chips, or white chocolate chips, instead of semi-sweet. Apart from chocolate chips, there are plenty of other additions you can make to your muffins. Some raisins would make a great addition to this Zucchini Muffin recipe. Or add some spices to go with the cinnamon like nutmeg, or cloves. Finally, you can fill the muffins with more fiber by adding a handful of old-fashioned oats.
  • Vegan: To make Healthy Zucchini Muffins non-dairy replace the chocolate chips with a dairy-free chocolate. You’ll also need to make the muffins egg-free. Replace the eggs in the recipe with flax eggs, applesauce, or mashed bananas.
  • Flour alternatives: If you don’t have whole wheat flour you can replace the wheat flour in the muffins with white whole wheat flour or all-purpose flour. You can also go with almond flour or oat flour for a gluten-free chocolate muffins.
  • Zucchini and Greek Yogurt Muffins: You can replace the apple sauce in the zucchini muffins with ¼ cup Greek Yogurt. You can also use half a cup sour cream. The slight sourness from these ingredients plays goes great with Healthy Zucchini Muffins, and make them extra moist.
  • Sweetener alternatives: Compared to other Chocolate Chip Zucchini Muffin recipes these muffins have a lot less sugar. But if you don’t want to use granulated sugar you can replace it with coconut sugar, turbinado sugar, brown sugar, or maple syrup.



  • Serve: Kept covered in a cool and dry place your Zucchini Muffins will stay good for 1-2 days at room temperature.
  • Store: Zucchini Muffins will stay good in a sealed bag or airtight container for up to a week in the fridge.
  • Freeze: This is a great recipe is completely freezer-friendly. Store the Healthy Chocolate Zucchini Muffins in a freezer bag separated by parchment paper. They’ll stay good in the freezer for 3 months. Defrost them in the fridge overnight for a on-the-go chocolate-y breakfast.

Muffin Tin with Chocolate Zucchini Muffins

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Chocolate Zucchini Muffins

Chocolate Zucchini Muffins are a moist, rich and fudgy kid-friendly breakfast, that you'd never guess is healthy. Made with whole wheat, applesauce, cinnamon, semisweet chocolate chips and zucchini.
Yield 12 Servings
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast
Cuisine American
Author Sabrina Snyder


  • 1/2 cup sugar
  • 2 tablespoons vegetable oil
  • 2 large eggs
  • 1 cup unsweetened applesauce
  • 1/4 teaspoon vanilla extract
  • 2 cups whole wheat flour
  • 2 tablespoons unsweetened cocoa powder
  • 1 1/4 teaspoon baking soda
  • 1 1/2 teaspoon ground cinnamon
  • 1/4 teaspoon sea salt
  • 1 1/2 cups shredded zucchini , about 2 medium zucchinis
  • 1/2 cup chocolate chips


  • Preheat oven to 350 degrees and line muffin tin with muffin liners.
  • Whisk together the sugar, oil, eggs, applesauce and vanilla extract in a large bowl.
  • Whisk together the flour, cocoa powder, baking soda, cinnamon, and salt. Gradually mix the dry ingredients into the wet ingredients.
  • Fold the shredded zucchini and chocolate chips into the batter until well combined.
  • Using a ¼ cup measure, add batter to muffin tin.
  • Bake for 18-20 minutes.


Calories: 184kcal | Carbohydrates: 31g | Protein: 4g | Fat: 6g | Saturated Fat: 3g | Cholesterol: 32mg | Sodium: 182mg | Potassium: 152mg | Fiber: 3g | Sugar: 15g | Vitamin A: 99IU | Vitamin C: 3mg | Calcium: 26mg | Iron: 1mg
Keyword: Chocolate Zucchini Muffins

Healthy Chocolate Zucchini Muffins collage

About the Author: Sabrina Snyder

Sabrina is a trained professional chef who has cooked for private clients for over a dozen years. Experienced in handling dietary restrictions, allergies and picky kid eaters, she's well versed in coming up with healthy, yet flavorful recipes.


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