Healthy Double Chocolate Zucchini Muffins
Bursting with rich chocolate flavor and sneaky veggies, these chocolate zucchini muffins are oh-so-delicious! They’re easy to whip up and guaranteed to win over even the pickiest taste testers!

Do you have a pile of zucchini taking over your kitchen counter right now? Same here. The rest of my garden is pretty mediocre this year, but my zucchini plant is apparently making up for everyone else’s poor performance. I promise, I only planted one plant, but it’s producing like crazy, and I CAN. NOT. KEEP. UP.
At first, I was feeling like a boss with my bounteous harvest. I love cooking up some good sautéed or grilled zucchini, but we’re reaching burnout levels on that. So, I’ve moved on to my favorite backup plan: baking.
The good news?
The beauty of baking with zucchini is that it’s a delicious way to use up a lot of it—plus my kids will happily eat their veggies when they’re hidden in muffins, quick breads, or even cake. In the past several weeks, I’ve baked classic zucchini bread, these popular superhero muffins, and this to-die-for chocolate cake…all of which have been a hit.
And yet, even after all that baking, I still have a mountain of zucchini staring me down. So I started thinking about other possibilities. My love of chocolate combined with the never-ending quest for hearty, kid-friendly after school snack options led to these ridiculously delicous muffins!

Why you’ll love these double chocolate zucchini muffins
If you’re like me, you loooove chocolate. But maybe you also want to fuel your body with (mostly) healthy food. So when you can enjoy that chocolatey goodness while sneaking in some veggies? It’s a win-win!
These Double Chocolate Zucchini Muffins take the classic muffin to a whole new level. They’re as rich and fudgy as any good dessert, but they are also packed full of vitamins and fiber (thank you whole grains and zucchini)!
With school starting back up, they’re perfect for tossing into lunchboxes or serving as an after-school snack. They’re also just as good at home on the breakfast table…or as a late-night treat.
So many options. Better make it a double batch.

Ingredients and Options
Here’s a peek at what you’ll need, and some tips for customizing the recipe to fit your needs:
- Flour: The recipe calls for a mix of whole wheat and all-purpose flour. For extra nutrition, you can use all whole wheat flour, but keep in mind that this will yield a denser texture. If you’re looking for an extra health boost, consider replacing 1/4 cup of flour with ground flaxseed (I do this in most of my baked goods). Flaxseed is a great source of Omega-3 fatty acids and fiber.
- Sweetener: I love using pure maple syrup in my baking to add a touch of natural sweetness and a rich flavor. Honey is a great substitute, or if you’re in a pinch, regular sugar will work, too.
- Oil/Butter: Butter adds a delicious richness, but coconut oil is a good alternative if you prefer. Just be mindful of its tendency to solidify in cooler temperatures.
- Veggies: Zucchini is the star here, but you can experiment with other veggies like carrots or sweet potatoes. Just make sure to keep the total veggie amount around 1 cup.
- Chocolate: For the chocolate chips, use your favorite type—dark, milk, or semi-sweet. You could even go wild with a mix of different chocolates!
How to store muffins
To keep these muffins at their best, store them in an airtight container at room temperature for up to two days. To prevent them from becoming soggy, place a paper towel under and over the muffins in the container. (Note: To limit condensation, make sure you let the muffins cool completely before placing them in a container for storage.)
For longer storage, freeze them! I often double my muffin recipes and freeze the extras. After they are completely cooled, place them in an airtight zip top bag an pop them in the freezer for up to a month (or more…you just risk freezer burn if they get lost in the back for too long).
Want your leftover muffins to taste like they just came out of the oven? Pop them in the toaster oven for a few minutes and they will be warm and delicious all over again.
Let’s get baking!
Healthy Double Chocolate Zucchini Muffins
Bursting with rich chocolate flavor and sneaky veggies, these chocolate zucchini muffins are oh-so-delicious! They're easy to whip up and guaranteed to win over even the pickiest taste testers!
Ingredients
- 1 cup whole wheat flour
- 1 cup all-purpose flour
- 2/3 cup cocoa powder
- 1/2 teaspoon baking soda
- 1 teaspoon baking powder
- 1/2 teaspoon salt
- 1/2 cup maple syrup (or honey)
- 1/4 cup melted butter (or coconut oil)
- 1/2 cup mashed banana (or applesauce)
- 1/2 cup milk (almond milk)
- 2 large eggs
- 1 teaspoon vanilla extract
- 2 cups finely shredded zucchini (about two medium zucchini, squeezed dry)
- 1/2 cup chocolate chips
Instructions
- Preheat your oven to 375°F. Line a muffin tin with paper liners or lightly grease it.
- In a medium bowl, whisk together the whole wheat flour, all-purpose flour, cocoa powder, baking soda, baking powder, and salt.
- In a large bowl, beat the maple syrup, melted butter, banana, milk, eggs, and vanilla extract until well combined.
- Stir in the shredded zucchini until evenly mixed.
- Gradually add the dry ingredients to the wet ingredients, mixing until just combined. Fold in the chocolate chips.
- Divide the batter evenly among the muffin cups, filling each about 3/4 full. I like to add a few extra chocolate chips to the tops of the muffins to make them look extra pretty, but that's optional.
- Bake for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
- Let the muffins cool in the tin for 5 minutes, then transfer them to a wire rack to cool completely.
Notes
To make mini muffins, reduce bake time to 12-14 minutes.
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Enjoy!

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