If you’re someone who loves rich, chocolatey treats but still tries to keep things wholesome, these fudgy chocolate zucchini muffins are going to be your new go-to. They’re everything you want in a chocolate muffin—decadent, moist, satisfying—yet they’re secretly packed with veggies and made entirely from clean, healthy ingredients. No gluten, no refined sugar, no problem.

This recipe is a brilliant way to sneak in some vegetables without sacrificing flavor. Thanks to ingredients like almond butter, shredded zucchini, and dark chocolate chips, each bite feels indulgent while being nourishing enough for breakfast or a healthy snack.

Fudgy Chocolate Zucchini Muffins (Healthy & Gluten-Free)

Why You’ll Love This Recipe

These chocolate zucchini muffins strike the perfect balance between healthy and delicious. They’re:

Incredibly fudgy and moist, thanks to almond butter, applesauce, and zucchini.
Kid-approved—your little ones won’t even notice the veggies.
Refined sugar free—naturally sweetened with maple syrup.
Gluten-free with nutrient-dense almond flour as the base.
Freezer-friendly, so you can make a batch and enjoy them all week.

Whether you need a quick breakfast on the go or a satisfying treat after dinner, these muffins fit the bill perfectly.

Ingredients

1 ¼ cup blanched almond flour
⅓ cup unsweetened cocoa powder
1 teaspoon baking soda
½ teaspoon kosher salt
1 large egg, lightly whisked
⅓ cup maple syrup
¼ cup unsweetened applesauce
¼ cup creamy almond butter
¼ cup non-dairy milk (such as almond or coconut milk)
1 tablespoon olive oil or coconut oil
1 teaspoon vanilla extract
1 cup shredded zucchini (excess moisture squeezed out)
⅔ cup chocolate chips (plus more for topping)

Tip: You can find the full list of ingredients and measurements in the recipe card below.

Instructions

Preheat your oven to 400°F and line a 12-cup muffin pan with liners. Set aside.
Shred the zucchini with a box grater. Place it in a clean kitchen towel and wring out all the excess moisture.
In a medium bowl, combine almond flour, cocoa powder, baking soda, and salt.
In a separate bowl, whisk together the egg, maple syrup, applesauce, almond butter, non-dairy milk, oil, and vanilla extract.
Combine the wet and dry ingredients and mix until smooth.
Fold in the shredded zucchini and chocolate chips.
Divide the batter evenly into the prepared muffin pan.
Sprinkle extra chocolate chips on top if desired.
Bake for 22–25 minutes or until a toothpick comes out mostly clean.
Let cool, then enjoy!

Variations

Nut-free version: Swap almond flour for oat flour and almond butter for sunflower seed butter.
Extra chocolatey: Add a tablespoon of espresso powder to deepen the chocolate flavor.
Make it vegan: Replace the egg with a flax egg (1 tablespoon ground flaxseed + 3 tablespoons water).

How to Store and Reheat

Storage: Store in an airtight container at room temperature for up to 3 days, or in the fridge for up to a week.

Freezing: These muffins freeze beautifully. Let them cool completely, then store in a freezer-safe bag or container for up to 3 months.

Reheating: Warm in the microwave for 15–20 seconds or reheat in a 300°F oven for about 5 minutes.

Frequently Asked Questions

What does zucchini do in chocolate muffins?

Zucchini adds moisture and softness to the muffins without affecting the flavor, making them ultra-fudgy and tender.

Can I taste the zucchini?

Not at all. Once baked, the zucchini virtually disappears in flavor and texture. All you’ll taste is chocolatey goodness.

Are these muffins gluten-free?

Yes! These are made with almond flour, which is naturally gluten-free.

Can I use a different flour?

You can try oat flour or a gluten-free flour blend, but results may vary since almond flour has a unique texture and fat content.

Are these muffins sweet enough for dessert?

Absolutely. They’re naturally sweetened but rich and decadent enough to feel like a treat.

Can I use honey instead of maple syrup?

Yes, though it may slightly alter the flavor and texture. Honey is sweeter and thicker than maple syrup.

Do I need to peel the zucchini?

No need to peel it. Just shred it and squeeze out the extra moisture before using.

Can I skip the chocolate chips?

You can, but they add a lot to the texture and flavor. Try using chopped dark chocolate or leave them out for a lighter version.

What can I use instead of applesauce?

Mashed banana or Greek yogurt can work in place of applesauce, but they will slightly change the taste.

How do I know when the muffins are done?

Insert a toothpick into the center of a muffin—if it comes out mostly clean with a few moist crumbs, they’re ready.

Conclusion

These chocolate zucchini muffins are a must-try whether you’re baking for picky kids, health-conscious friends, or just yourself. Rich, chocolaty, and made with clean, whole ingredients, they’re the kind of treat you’ll feel good about eating any time of day. Try them once and you’ll be hooked.