Moist, rich, and packed with deep chocolate flavor, these Chocolate Zucchini Muffins are a fun and tasty way to sneak in veggies while satisfying your sweet tooth. Perfect healthy treat for breakfast, as a snack, or even dessert!
This post may contain affiliate links. As an Amazon Associate, I earn from qualifying purchases. Please see my disclosure policy for details.
Table of Contents
You'll never guess these are healthy Chocolate Zucchini Muffins–loaded with dreamy chocolate-cake-like flavor, yet made with vegetables and good-for-you ingredients. Between the cakey texture, bursts of melty chocolate chips, and the subtle warming spice of cinnamon, these muffins hit all the right notes. Fresh shredded zucchini keeps them perfectly moist without overpowering the taste, while applesauce and Greek yogurt work double-duty to lighten the crumb and add an irresistible moist texture.
These zucchini chocolate muffins are everything I want in a snack: rich in chocolate flavor, soft, satisfying, and easy to whip up on a weekday. They're made with wholesome ingredients, but still give classic chocolate chip muffins a run for their money. If you're looking for muffin recipes that your whole family will devour–without realizing there are vegetables inside–this one is for you!
Even better? These double chocolate zucchini muffins come together quickly and freeze beautifully, making them perfect for adding to school lunches, enjoying as an afternoon snack, or a chocolatey dessert treat. The rich cocoa powder, hints of vanilla, and mini chocolate chips pair effortlessly with the subtly sweet zucchini to bring a craveable combination of flavors to every bite. It's a muffin recipe you'll make again and again.
Do you love baking with zucchini? Me too! Check out my other zucchini sweet treats: Zucchini Cake, Banana Zucchini Bread, Zucchini Blueberry Muffins, Zucchini Carrot Bread, and Gluten-Free Zucchini Bread.
Why You'll Love Chocolate Zucchini Muffins
These healthy chocolate chip zucchini muffins check all the boxes–rich, satisfying, and secretly packed with veggies. Here's why you'll be making them on repeat:
- Rich Flavor, Healthier Ingredients - Using unsweetened applesauce, Greek yogurt, and shredded zucchini gives these muffins an incredible, rich, and moist texture without needing tons of oil.
- Kid-Approved, Freezer-Friendly - They're perfect for easy meal prepping and make great lunchbox or after-school snacks.
- Easily Customizable - Get creative with additional add-ins or variations–these muffins can do it all with simple substitutions.
Ingredients and Substitutions
Zucchini - Freshly shred a zucchini using a box or handheld vegetable grater. Then, squeeze out the excess moisture with a paper towel before adding to the batter.
Unsweetened Cocoa Powder - Use a high-quality 100% natural cocoa powder to give this chocolate zucchini muffins recipe its signature chocolatey color and flavor.
Greek Yogurt - Choose plain or vanilla depending on your preference, to add extra creaminess and moistness.
Unsweetened Applesauce - Adds natural sweetness and moisture without an overly sugary punch. Swap 1:1 with equal parts mashed banana or Greek yogurt if needed.
Oil - I prefer using avocado oil for its abundance of healthy fats, though you can also use canola or grapeseed oil. Or, use melted coconut oil for a richer flavor.
Eggs - Two large eggs at room temperature help mind the muffins and provide texture.
Vanilla Extract - Use pure vanilla extract to add warmth and enhance the chocolate flavors.
Sugars - A combination of light brown sugar and white sugar adds the perfect sweetness and contributes to a moist, soft muffin texture. For a lower-glycemic option, substitute with coconut sugar.
Flour - Use all-purpose flour or whole wheat pastry flour for added fiber. Or use a 1:1 gluten-free flour blend for those with dietary restrictions.
Baking Powder & Baking Soda - These leveling agents help the muffins rise to fluffy perfection.
Fine Sea Salt - Helps balance the sweet, rich flavors. Himalayan pink salt also works.
Ground Cinnamon - Adds a lovely warmth and depth to the flavor. Omit if preferred.
Mini Chocolate Chips - For a classic double chocolate muffin experience, use regular chocolate chips, or dark chocolate for a richer taste.
How to Make Chocolate Zucchini Muffins
For the complete recipe, measurements, and instructions, scroll to the recipe card at the bottom of this post.
Step 1: Preheat the oven to 350°F and move the baking rack to the center of the oven. Line 2 cupcake pans with 12 cupcake liners, adding the liners to every other cup. Brush the top of the cupcake pans around each liner with oil or butter to help the muffins release more easily from the pan.
Step 2: In a large mixing bowl, whisk the oil, yogurt, applesauce, eggs, vanilla extract, brown sugar, and white sugar until combined.
Step 3: Place the shredded zucchini on a dish towel or stack of clean paper towels. Fold up the ends of the towel and squeeze the excess moisture from the zucchini. Discard the moisture.
Step 4: Add the drained zucchini to the wet ingredients. Stir until well combined.
Step 5: In a small bowl, whisk the flour, cocoa powder, baking powder, baking soda, and salt together until combined.
Step 6: Add the dry ingredients to the wet ingredients. Stir until just combined.
Step 7: Add ½ cup of the chocolate chips to the batter. Gently fold in until just combined.
Step 8: Scoop the batter into the muffin cups, dividing it evenly between them (about ⅓ cup per muffin cup). Sprinkle 1 teaspoon of the remaining chocolate chips on top of each muffin.
Step 9: Bake the muffins for 18-22 minutes or until a toothpick inserted into the center of the muffins comes out clean. Cool the muffin trays on a wire rack on the counter. Enjoy!
Recipe Pro-Tips
- Squeeze the zucchini well. Removing as much moisture as possible from the shredded zucchini is key to avoiding soggy and flavorful muffins. Wrap the shredded zucchini in a clean dish towel or paper towels and squeeze out the excess moisture.
- Avoid over-mixing the batter. Once you add the dry ingredients to the wet, gently stir until just combined to maintain a tender texture. Over-mixing can lead to a tough texture.
- Line every other muffin tin cup. This helps heat distribute more evenly, ensuring the best rise. It also prevents the muffin tops from sticking together. It's one of my favorite baking hacks!
- Mind the baking time. Keep an eye on the baking time, checking the muffins around 18 minutes and adding more time if needed. The muffins are done when a toothpick inserted into the center comes out clean.
- Serve with toppings. Enjoy warm or at room temperature with a spread of peanut butter, butter, or coconut oil for an extra indulgent touch. It's also great with a warm mug of brewed coffee or a protein coffee latte!
Recipe Variations
- Dark Chocolate: Use dark cocoa powder and dark chocolate chips for extra chocolatey depth–this one's for the chocolate lovers!
- Gluten-Free: Use a 1:1 gluten-free flour blend, then let the cupcake batter sit for 30 min before baking to create the best texture.
- High-Protein: Reduce the flour by ¼ cup and add ½ cup of chocolate protein powder into the dry ingredients.
- Chocolate Zucchini Bread: Pour the batter into a greased 8x4-inch loaf pan and bake for 50-60 minutes or until a toothpick inserted in the center comes out clean.
- Dairy-Free/Vegan: Swap the Greek yogurt with dairy-free coconut yogurt or another plant-based yogurt and use dairy-free chocolate chips for a dairy-free version. To make these muffins completely vegan, swap the eggs for flax eggs: 2 tablespoons of flaxmeal combined with 6 tablespoons of water. Let it sit for 5-10 minutes to gel before adding.
- Extra Veggies: Swap ½ cup of the shredded zucchini for shredded carrots to add a natural sweetness and boost of color and nutrition.
- Nutty: Fold in ¼ cup of chopped nuts like walnuts or pecans for even more texture and a buttery crunch.
Storage Directions
- Storing: Allow the muffins to cool completely before storing in an airtight container at room temperature for 3 days, or up to 5 days in the refrigerator.
- Freezing: Once cooled, transfer to a freezer-safe, airtight container. Freeze for up to 3 months. Thaw at room temperature for 1-2 hours or reheat from frozen in the microwave for 20-30 seconds.
FAQs
Nope! Just wash, dry, and grate it-no peeling necessary. The skin is thin and softens perfectly while baking, plus it adds fiber and nutrients.
Zucchini holds a lot of water, which can make the batter too wet. Squeezing out the excess moisture ensures fluffy, moist muffins instead of soggy ones.
Absolutely, and it's great for meal prep! Cool the muffins completely, store in a freezer-safe, airtight container, and freeze for up to 3 months.
You can! Just keep in mind that liquid sweeteners can affect the batter's texture–reduce the applesauce slightly or add 1-2 tablespoons of extra flour.
Save this Recipe for Later on Pinterest
Tools Needed to Make This Recipe
- Muffin Tray
- Muffin Liners
- Paper Towels or a Dish Towel
- Large & Small Mixing Bowls
- Whisk
- Rubber Spatula
- Wire Cooling Rack
- Measuring Cups & Spoons
More Healthy Muffin Recipes
- Rhubarb Muffins
- Peach Muffins
- Banana Zucchini Muffins
- Zucchini Carrot Muffins
- Healthy Blueberry Muffins
- Kodiak Protein Muffins
- Banana Pumpkin Muffins
- Healthy Banana Muffins
Recipe Card
Chocolate Zucchini Muffins
Ingredients
- ½ cup avocado oil canola, or grapeseed oil
- ⅓ cup unsweetened applesauce
- ½ cup vanilla or plain Greek yogurt
- 2 large eggs brought to room temperature
- 1 teaspoon pure vanilla extract
- 2 tablespoons packed light brown sugar
- ¾ cup white sugar
- 1 ½ cups shredded zucchini
- 1 ¾ cups (220g) all-purpose flour or whole wheat pastry flour
- ½ cup cocoa powder
- 1 teaspoon baking powder
- ½ teaspoon baking soda
- ¼ teaspoon fine sea salt
- 1 teaspoon ground cinnamon
- ¾ cup mini chocolate chips divided
Instructions
- Preheat the oven to 350°F and move the baking rack to the center of the oven. Line 2 cupcake pans with 12 cupcake liners, adding the liners to every other cup. Brush the top of the cupcake pan around each liner with oil or butter to help the muffins release more easily from the pan.
- In a large mixing bowl, whisk the oil, yogurt, applesauce, eggs, vanilla extract, brown sugar, and white sugar until combined.
- Place the shredded zucchini in a dish towel or stack of clean paper towels. Fold up the ends of the towel and squeeze the excess moisture from the zucchini. Discard the moisture.
- Add the drained zucchini to the wet ingredients. Stir until well combined.
- In a small mixing bowl, whisk the flour, cocoa powder, baking powder, baking soda, and salt together until combined.
- Add the dry ingredients to the wet ingredients. Stir in until just combined.
- Add ½ cup of the chocolate chips to the batter. Gently fold in until just combined.
- Scoop the batter into the muffin cups, dividing it evenly between them (about ⅓ cup per muffin cup). Sprinkle 1 teaspoon of the remaining chocolate chips on top of each muffin.
- Bake the muffins for 18-22 minutes or until a toothpick inserted into the center of the muffins comes out clean.
- Cool the muffin trays on wire cooling racks for 5-10 minutes or until the muffins are cool enough to touch. Remove the muffins from the pan and cool directly on the wire rack until room temperature. Enjoy!
Notes
- Storing: Allow the muffins to cool completely before storing in an airtight container at room temperature for 3 days, or up to 5 days in the refrigerator.
- Freezing: Once cooled, transfer to a freezer-safe, airtight container. Freeze for up to 3 months. Thaw at room temperature for 1-2 hours or reheat from frozen in the microwave for 20-30 seconds.
- Squeeze the zucchini well. Removing as much moisture as possible from the shredded zucchini is key to avoiding soggy and flavorful muffins. Wrap the shredded zucchini in a clean dish towel or paper towels and squeeze out the excess moisture.
- Avoid over-mixing the batter. Once you add the dry ingredients to the wet, gently stir until just combined to maintain a tender texture. Over-mixing can lead to a tough texture.
- Line every other muffin tin cup. This helps heat distribute more evenly, ensuring the best rise. It also prevents the muffin tops from sticking together. It's one of my favorite baking hacks!
- Mind the baking time. Keep an eye on the baking time, checking the muffins around 18 minutes and adding more time if needed. The muffins are done when a toothpick inserted into the center comes out clean.
