These healthy chocolate zucchini muffins are incredibly moist, rich, and loaded with chocolate chips! Made with almond flour, they’re naturally gluten free, grain free, dairy free and paleo, with hidden veggies in every bite.
If you’re looking for the perfect way to use up fresh summer zucchini, these healthy chocolate zucchini muffins are about to become a new favorite!
They’re moist, rich and chocolatey, made with wholesome ingredients like almond flour, cocoa powder and fresh zucchini, with plenty of melty chocolate chips in every bite!
Even better, these muffins are naturally gluten free, grain free, dairy free and paleo, making them a delicious option for breakfast, snacks or dessert.
The zucchini keeps every muffin soft and tender without adding a noticeable vegetable flavor, so they’re a great way to sneak extra veggies into something everyone will happily eat.
Whether you’re baking during zucchini season or simply craving a healthier chocolate muffin, this easy one-bowl recipe comes together quickly and freezes beautifully for meal prep!
Why You’ll Love These Healthy Chocolate Zucchini Muffins
These muffins check every box for a delicious homemade treat:
- Rich double chocolate flavor with plenty of chocolate chips
- Extra moist thanks to fresh shredded zucchini
- Naturally gluten free, grain free and dairy free
- Paleo-friendly ingredients
- Easy one-bowl recipe
- Great for breakfast, snacks or dessert
- Kid-approved
- Freezer friendly
- A delicious way to use summer zucchini
Unlike many healthy muffins that can turn out dry or dense, these stay soft for days thanks to the combination of almond flour, almond butter and zucchini.
Ingredients You’ll Need for These Zucchini Muffins
Everything in this recipe is simple and easy to find, and if you’re familiar with grain free baking you probably have most of them in your pantry!
Here’s everything you’ll need to make double chocolate zucchini muffins:
Almond Flour + tapioca or arrowroot
Blanched almond flour along with tapioca or arrowroot flour creates a soft, tender crumb while keeping the muffins naturally grain free and gluten free.
Cocoa Powder or cacao powder
Unsweetened cocoa powder gives the muffins their rich chocolate flavor.
Coconut Oil
For moistness and richness
Almond Butter
Adds richness, healthy fats and helps create a moist texture.
Maple Sugar or Coconut Sugar
Both work well for naturally sweetening the muffins.
Eggs
Eggs provide structure while keeping the muffins light.
Zucchini
Fresh shredded zucchini makes these muffins incredibly moist without making them taste like vegetables.
Chocolate Chips
Dark dairy-free chocolate chips create pockets of melted chocolate throughout each muffin.
How to Make Healthy Chocolate Zucchini Muffins
These muffins couldn’t be easier.
- Preheat the oven and prepare your muffin pan.
- Whisk together the dry ingredients.
- Whisk the wet ingredients until smooth.
- Stir the dry ingredients into the wet ingredients.
- Fold in the shredded zucchini and chocolate chips.
- Divide the batter evenly among the muffin cups.
- Sprinkle additional chocolate chips on top.
- Bake until the tops are set and a toothpick comes out mostly clean.
- Cool before serving.
Tips for Perfect Chocolate Zucchini Muffins
Squeeze the zucchini well
Removing excess moisture keeps the muffins fluffy rather than dense.
Don’t overmix
Mix only until combined to keep the crumb tender.
Top with extra chocolate chips
This creates bakery-style muffins and makes them even prettier!
Let them cool
The texture improves after about 15 minutes of cooling.
Variations
Customize these muffins with simple additions!
- Chopped walnuts
- Chopped pecans
- Dairy-free white chocolate chips
- Espresso powder for deeper chocolate flavor
- Mini chocolate chips
- Sprinkle flaky sea salt on top after baking
Storage
Store covered at room temperature for up to 2 days or refrigerate for up to 5 days.
Freeze for up to 3 months. Thaw overnight in the refrigerator or warm briefly in the microwave before serving.
Frequently Asked Questions
Do chocolate zucchini muffins taste like zucchini?
No, not at all! The zucchini simply keeps the muffins moist and tender. You won’t notice a vegetable flavor.
Do I need to peel the zucchini?
No. The peel is very thin and softens during baking. You can peel it if you prefer.
Should I squeeze the zucchini?
Yes. Removing excess moisture helps the muffins bake evenly and keeps the texture from becoming too wet.
Can I make these dairy free?
Yes. Simply use dairy-free chocolate chips.
Can I freeze these muffins?
Absolutely! Once completely cooled, freeze them in an airtight container for up to three months.
Are these muffins paleo?
Yes! They’re made with almond flour, naturally sweetened with maple sugar or coconut sugar, and contain no grains or dairy.
Can I make these with yellow squash?
Yes. Yellow summer squash works just as well and has a very similar texture.
These healthy chocolate zucchini muffins are proof that wholesome baking can still taste incredibly indulgent!
Rich, moist and loaded with chocolate chips, they’re the perfect way to use fresh zucchini while making a snack or breakfast everyone will love.
Whether you’re baking a batch for busy weekday mornings, packing lunches or freezing extras for later, these grain free muffins are easy to make and even easier to enjoy.
Once you try them, they’ll quickly become one of your favorite healthy zucchini recipes!
More Healthy Zucchini Recipes
If you have extra zucchini to use, be sure to try these favorites:
- Double Chocolate Zucchini Bread
- Blueberry Zucchini Muffins
- Chocolate Chip Zucchini Bread
- Zucchini Coffee Cake Muffins
- Zucchini Banana Bread
- Zucchini Fritters with Bacon
Healthy Chocolate Zucchini Muffins (Gluten Free, Paleo)
Ingredients
- 1 1/2 cups blanched almond flour
- 1/4 cup tapioca flour or arrowroot
- 1/2 cup cocoa powder or raw cacao
- 1 tsp baking soda
- 1/2 tsp baking powder optional, but highly recommended if not Whole30
- 1/4 tsp fine sea salt
- 1/4 cup refined coconut oil melted and cooled
- 1/4 cup smooth almond butter or cashew butter
- 3/4 cup maple sugar or coconut sugar
- 3 large eggs room temperature
- 1 tsp vanilla extract
- 2 medium zucchini finely shredded, moisture squeezed out well (about 1 1/2-2 cups after squeezing)
- 2/3 cup dark chocolate chips plus a few extra for topping
Instructions
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Preheat your oven to 350°F. Line a 12-cup muffin pan with paper liners or grease well.
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In a medium bowl whisk together the almond flour, tapioca flour, cocoa powder, baking soda, baking powder, salt
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In a large bowl whisk together the coconut oil, almond butter, maple sugar, eggs and vanilla until completely smooth.
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Stir the dry ingredients into the wet ingredients just until no dry streaks remain.
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Gently fold in the zucchini, then the chocolate chips.
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Divide evenly among the muffin cups, filling each about 90% full to make 12 muffins. Sprinkle a few chocolate chips on the top of each.
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Bake 22-25 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs (melted chocolate is fine).
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Cool in the pan for 10 minutes, then transfer to a wire rack to fully cool. Enjoy!
Recipe Notes
*Store covered at room temperature for up to 2 days or refrigerate for up to 5 days.
**Freeze for up to 3 months. Thaw overnight in the refrigerator or warm briefly in the microwave before serving.
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