Gluten-Free Chocolate Zucchini Muffins

These decadent yet healthy gluten-free chocolate zucchini muffins are packed with nourishing ingredients that even the pickiest of eaters can’t taste!

Gluten-Free Chocolate Zucchini Muffins

If you’re on the hunt for the perfect chocolate zucchini muffin recipe, look no further. These gluten-free and double-chocolate treats are kiddo and adult-approved and you’ll likely find yourself needing to make a double batch so they’re not gone in a flash. Here’s the scoop on what makes these double chocolate zucchini muffins special and some tips on making them turn out just right.

Double Chocolate Zucchini Muffins

Do you have to peel the zucchini?

Nope! Whether you’re shredded or grating, the peel won’t affect the batter or muffin crumb- it basically just melts into the muffin while cooking. The most important step is just making sure you drain/squeeze the zucchini after you’ve shredded or grated it.

What ingredients do I need for chocolate zucchini muffins?

Gluten-Free flour: (I like Bob’s Red Mill 1:1 Baking Flour or any other GF flour blend that already has xanthum gum added). If you’re new to gluten-free baking, you can learn more about xanthum gum here.

Unsweetened cocoa powder: You can also use “cacao” powder but it will have a slightly richer chocolate taste.

Avocado oil: it’s been my favorite for baking lately) or melted butter if you want a slightly creamier and not dairy-free muffin.

Maple syrup: you’ll only need 1/3 cup for the whole recipe- no sugar rush here! 

Egg: You *could* sub a flax egg but it will slightly compromise the texture and reduce the protein content a smidge.

Shredded or grated zucchini: DRAIN and squeeze (put a paper towel under/around) and squeeze until all the liquid runs out.

Pumpkin puree: I used pumpkin puree because it’s the season where I almost always have extra in a mason jar in the fridge, but you can easily sub applesauce or mashed banana!

Almond milk or milk of choice- I’ve actually been on an oat milk kick lately!

Chocolate chips; dairy free if desired, and you can choose regular or mini. I like regular size because they don’t melt as fast and you get ooey-gooey chocolate bites that way!

How long will zucchini muffins stay fresh?

About two days on the countertop but at least five days, if kept in the fridge. The moisture content from the zucchini can definitely cause these to spoil faster. It’s hard for us to keep a batch around the house longer than two days anyway ;).

Should I hide zucchini in muffins or other baked goods?

Making zucchini muffins has long been a trick for many moms to get their kiddos (or even husbands) to eat some extra veggies. As a pediatric dietitian, I value the nutrition in veggies but I also value informed consent and don’t actually recommend “sneaking” veggies into dishes as it can break trust. I feel that disclaimer is necessary after working with so many families of picky eaters and understanding the important of trust in the feeding relationship. I don’t say the above lightly- I know firsthand the struggle of getting veggies into littles!

Chocolate Zucchini Muffins

KISS Tip: You could easily swap out yellow squash in these muffins without noticing a significant flavor difference.

KISS Tip: Make a double batch and freeze some of the extra for a quick breakfast or snack on the go!

That close up shows how you can’t even see the green vegetable in these chocolate zucchini muffins!

Double Chocolate Muffins with Hidden Zucchini

Thank you for following along with this muffin series! If you missed last week’s Chai Spiced Apple Muffins, definitely check them out- there’s already save 5 star ratings on there. Next up will be Trail Mix Muffins and I think I’m most excited about those- they’ll be perfect for a Halloween treat!

Print Recipe
5 from 3 votes

Gluten-Free Chocolate Zucchini Muffins

Prep Time15 mins
Cook Time20 mins
Total Time35 mins
Servings: 12 muffins


  • 12-cup muffin tin
  • 12 muffin liners


Dry Ingredients

  • 1 1/4 cup gluten-free flour
  • 1/3 cup unsweetened cocoa powder
  • 1 tsp baking soda
  • 1/4 tsp salt

Wet Ingredients

  • 2 Tbsp avocado oil or melted butter
  • 1/3 cup maple syrup
  • 1 tsp vanilla
  • 1 egg
  • 1/4 cup pumpkin puree or applesauce
  • 1/2 cup almond milk or milk of choice

Other Ingredients

  • 1 cup shredded zucchini, liquid drained (from about one large zucchini)
  • 1/2 cup regular or mini chocolate chips (dairy free is desired)


  • Preheat oven to 350 degrees. Line a 12-cup muffin tin with cupcake liners and spray inside of liners with oil.
  • Grate zucchini into a bowl and squeeze with paper towel to drain out any excess liquid- you want it as dry as possible!
  • In a medium bowl, whisk together flour, cocoa powder, baking soda, and salt.
  • In another bowl, mix the oil, maple syrup, vanilla, egg, almond milk, and pumpkin puree.
  • Once the wet ingredients are well mixed (use a whisk or hand mixer), slowly add in zucchini followed by the dry ingredients. Mix until just combined.
  • Fold in chocolate chips. Then, using a ¼ cup or ice cream scoop, spoon batter into prepared liner until about ¾ full. Bake 20-22 minutes or until toothpick inserted into middle comes out clean. After 5 minutes, remove muffins and transfer to wire rack to finish cooling. Enjoy!

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2 Responses

  1. 5 stars
    So good! This recipe was not only simple, but super fun to make with the kids. My oldest loved grating and squeezing the water out of the zucchini. And the flavor and texture are incredible. We made a double batch and I am glad we did. These will not last long for our family of five.

    1. Thank you so much for letting me know how much y’all enjoyed them! I’m so glad it was a fun recipe to make as a family and hopefully it can be a go to for years to come. Thanks, Becca!

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Welcome to KISS in the Kitchen! I’m Shannon, and my dad always told me “Keep it simple, Shannon”. And that’s what you’ll find here- simple recipes and simple ideas to help you get healthier and happier. Read more…



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