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Gluten-Free Zucchini Muffins

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by Lindsay Cotter Updated: Jul 04, 2025

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A stack of 3 gluten and dairy-free zucchini muffins with a text overlay for pinterest.

Made with fresh produce, dark chocolate chips, and a blend of gluten-free flours, these Zucchini Banana Muffins are soft, fluffy, and naturally sweetened! Whip up a batch in no time for healthy breakfasts, quick snacks, and more. Dairy-free. 

a stack of three chocolate chip gluten free zucchini muffins on top of each other this for later

  • Up to Our Eyeballs in Zucchini!
  • Ingredients for Zucchini Muffins
  • Tips & Tricks
  • Step-By-Step Instructions
  • Storage for Leftover Zucchini Muffins
  • Gluten-Free Muffin Recipes

Up to Our Eyeballs in Zucchini!

With late summer in full swing, we’re up to our eyeballs in fresh zucchini. But with recipes like Three Herb Tomato Zucchini Salad and Green Chile Tuna Zucchini Casserole, we think that’s a good thing!

However, while we love a good savory recipe, we can’t help but want something a little sweet every once in a while. So, what better way to use up some of that zucchini than with fresh baked muffins?

Ingredients for Zucchini Muffins

In addition to a few standard muffin ingredients like baking powder, baking soda, salt, and eggs, there are a few items you will need.

overhead image of ingredients for gluten free zucchini muffins including non-dairy milk, oat flour, almond flour, shredded zucchini, an egg, and two ripe bananas
  • Oat and Almond Flours – Great on their own in recipes like Flourless Honey Oat Ricotta Muffins and  Coconut Almond Flour Banana Muffins, these gluten-free flours are even better when combined! The fat content from the almond flour helps keep these zucchini muffins moist while the oat flour helps create a fluffier texture and incredible taste. We love using this flour blend in cookies as well! 
  • Cinnamon and Vanilla Extract – These help enhance the natural sweetness of the muffins.
  • Flax Meal – This not only provides a boost of fiber and healthy fats but also helps baked goods like zucchini muffins and apple oatmeal muffins retain their shape with plenty of fluff.
  • Banana – Full of antioxidants and rich in vitamin C and potassium, we swear by using mashed bananas when making waffles for a hint of sweetness without the need for refined sugar. Turns out, they work in muffins to replace the egg or oil found in most muffins, too!
  • Almond Milk – Just like any baked good, milk is used to thin out the batter. We love almond milk or oat milk, too!
  • Large Egg or Flax Egg– If you’re using a flax egg, add with the rest of the wet ingredients (mashed banana, milk, oil, etc.) and whisk together before adding the dry ingredients.
  • Honey or Maple Syrup – A natural substitute for refined sugar, honey adds a hint of sweetness and helps hold the rest of the ingredients together. Or, for a vegan option, use honey instead.
  • Zucchini – Of course, you can’t have a zucchini muffin recipe without zucchini! Just as in this bread, it provides a boost of moisture, plenty of vitamins, and lots of fiber to keep you full. Even better, it’s one of the most neutral-tasting vegetables you can find. This means that even the pickiest of eaters will have zero complaints.
  • Dark Chocolate Chips and Other Optional Add-Ins – There’s never a bad time for dark chocolate, right? However, feel free to experiment with all your favorite flavor add-ins like chopped nuts, dried fruit, or even a pinch of nutmeg. 

Tips & Tricks

More than your average muffin, there are a few tips and tricks that will help your muffins come out delicious and fluffy. You wouldn’t even know they are gluten-free.

  • Grate and Squeeze Your Zucchini – This is crucial to achieving the right texture! No need to peel the skin. A hydrating vegetable, zucchini is naturally full of water, which is great when using it on its own. However, when it comes to baked goods, this excess moisture will leak out, creating soggy muffins. For easy squeezing, we recommend using a cheesecloth, but a towel would work, too. 
  • Include Room Temperature Eggs. This allows for easier blending and helps the batter rise, creating the ultra fluffy muffin texture we love. 
  • Use Liners. Silicone, foil, or paper liners make prevent your muffins from sticking and make for easy cleanup and a pretty presentation! 
  • Fill Your Muffin Tins ⅔ of the Way Full. There’s no use crying over spilled muffins! Or, however the saying goes. Filling the muffin tin all the way to the top will lead to your batter spilling over and potentially burning on the pan. To prevent this from happening use a cookie scoop or spoon to fill each cup. 

Step-By-Step Instructions

  • Preheat your oven to 350° Fahrenheit, and grease a muffin pan with cooking spray. 
  • Use a cheese grater to shred the zucchini, and squeeze out any excess moisture. You’ll want to start with 1 full cup of grated zucchini, but it should reduce down to ¾ cup. See our notes below! 
  • Whisk together the dry ingredients in a medium bowl. 
The wet and dry ingredients for lemon zucchini bread.
clear bowl of egg and mashed banana batter with grated zucchini on top
  • In a separate large bowl, mash the banana. Then, whisk in the wet ingredients and fold in the shredded zucchini. 
  • Add the dry ingredients to the bowl with the wet ingredients for easier mixing. Then, stir until just combined. Do not overmix! Your muffins will become tough and rubbery if you do.  
a woman's hand holding a cookie scoop full of batter over a glass bowl of gluten free zucchini muffin batter
overhead image of a muffin tin full of unbaked gluten free zucchini muffin batter in white linters
  • Fold in the chocolate chips or any extras you want to include. Spoon the batter into a prepared muffin tin. 
  • Bake for 15-20 minutes or until a toothpick can be inserted and comes out clean. Cool in the pan for 5-10 minutes before transferring to a wire rack. 
two hands holding a muffin tin with 8 baked gluten free zucchini muffins topped with chocolate chips
a muffin pan full of 7 baked gluten free zucchini muffins and a single muffin on the side with the liner pulled down and a bite taken out

Storage for Leftover Zucchini Muffins

Before you store your muffins, be sure to let them cool completely. We know it’s tempting to dig in right away, but it’s worth the wait! As they cool, they’ll continue to bake. So, removing them from the pan too soon will cause them to crumble and fall apart. 

If you plan to eat your muffins right away, they can be stored in an airtight container at room temperature for up to 2 days. However, for longer-lasting muffins, you’ll want to store them in the fridge where they’ll keep for up to 1 week! 

To freeze the muffins, just place them in an airtight container or sealable bag, and store them in the freezer for up to 2 months. Then, when you’re ready to eat, thaw them in the microwave or refrigerator overnight. 

a woman's hand holding a chocolate chip gluten free zucchini muffin with a bite taken out

More of Our Favorite

Gluten-Free Muffin Recipes

  • Healthy Carrot Cake Muffins
  • Flourless Chocolate Chip Protein Muffins
  • Breakfast Muffins with No Added Sugar
  • Low-FODMAP Blueberry Muffins
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a close up image of a dairy free gluten free zucchini muffin with chocolate chips in a white muffin liner

Gluten-Free & Dairy-Free Zucchini Muffins


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5 from 3 reviews

  • Author: Lindsay Cotter
  • Total Time: 38-50 minutes
  • Yield: 10–12 muffins 1x
  • Diet: Gluten Free
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Description

Fluffy, moist, and naturally sweetened, Dairy Free Gluten-Free Zucchini Muffins are made made even better with bananas and chocolate chips for a breakfast or snack you can feel good about! Dairy Free.


Ingredients

Units Scale
  • 1 cup grated/shredded zucchini (¾ cup after water squeezed out)
  • 1 ⅓ to 1 ½ cups (150 grams) gluten-free oat flour
  • ⅓ cup (42 grams) blanched fine almond flour
  • 2 teaspoons baking powder
  • 1 teaspoon baking soda
  • ¼ teaspoon salt
  • 1 teaspoon cinnamon
  • 2 Tablespoons flax meal
  • ¾ cup (165 grams, ~ 1 large banana) mashed ripe banana
  • 1 large egg, room temperature (or flax egg, see notes)
  • ¼ cup non-dairy milk
  • ⅓ cup maple syrup or honey
  • 1 teaspoon vanilla extract
  • ¼ cup dark chocolate chips + more for topping

Instructions

  1. Preheat the oven to 350° F. Line or grease a muffin tin, and set aside.
  2. Shred the zucchini. Place shreds in a paper towel or cheesecloth, and gently squeeze out all excess water. Note – Once squeezed, the zucchini should reduce down to ¾ cup. 
  3. In a mixing bowl, whisk together the dry ingredients (oat flour, almond flour, baking powder, baking soda, salt, cinnamon, flax meal). 
  4. In a second large bowl, mash the banana. Mix in the remaining wet ingredients (zucchini, egg, milk, maple syrup, vanilla extract). 
  5. Working in batches, combine the dry ingredients to the bowl with the wet, and mix until combined. Do not overmix! Fold in the chocolate chips. (See notes)
  6. Spoon the batter into the prepared muffin tin, filling ⅔ – ¾ of the way full. Sprinkle extra chocolate chips on top, if desired.
  7. Bake for 17-22 minutes or until the center comes out clean with a toothpick. 
  8. Allow muffins to cool in the pan for 5-10 minutes before transferring to a wire rack to finish cooling. 

Notes

Substitutes: Flax Egg- Replace egg in recipe by whisking together 1 Tablespoon ground flaxseed and 2 ½ Tablespoons water. Set mixture aside for 5-10 minutes to thicken. Whisk the gelled mixture in with the other wet ingredients before adding the dry ingredients. This helps it blend evenly and gives the muffins better structure. Baking time and texture will vary.

Storage: Keep leftover muffins in the fridge for up to 2 weeks or freezer for up to 4 months. 

Texture Tip – For fluffier more moist muffins, let the batter sit for 10-20 minutes before spooning into muffin pan.

  • Prep Time: 10 minutes
  • Rest Time: 10
  • Cook Time: 18-20 minutes
  • Category: Breakfast, snacks
  • Method: Oven
  • Cuisine: American

Nutrition

  • Serving Size: 1 muffin
  • Calories: 136
  • Sugar: 8 g
  • Sodium: 181 mg
  • Fat: 2.6 g
  • Saturated Fat: 0.3 g
  • Carbohydrates: 22.4 g
  • Fiber: 2.8 g
  • Protein: 3.2 g
  • Cholesterol: 16.9 mg

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Categories: Baked Goods, Breakfast & Brunch, Dairy-Free, Egg-Free, Gluten-Free, Nightshade-Free, Oven, Snacks & Appetizers, Vegan, Vegetarian Tags: breakfast, dairy free, dairy free muffins, gluten free breakfast, gluten free muffins, gluten free snack, meal prep, muffin, muffins, snacks, vegan, vegetarian, zucchini, zucchini muffins

A stack of 3 gluten and dairy-free zucchini muffins with a text overlay for pinterest.
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Lindsay Cotter of Cotter Crunch

About Lindsay

Hi, y’all, I’m Lindsay Cotter, a Nutrition Specialist with a focus on Gluten-Free eating. I love creating delicious nourishing food that anyone can enjoy.

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A stack of 3 gluten and dairy-free zucchini muffins with a text overlay for pinterest.
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  1. Avatar photoVicki

    Aug 18, 2024 at 2:59 PM

    These turned out great. Delicious and undetectably GF. Bonus that they aren’t overly sweet like so many muffins.

    Reply
    • Avatar photoSammi (Cotter Crunch Test Kitchen)

      Aug 19, 2024 at 7:48 AM

      We are so glad you enjoyed them and no one can tell they are gluten free! 😉 And yes, love that their sweetness is just right. Happy baking!

      Reply
  2. Avatar photoJulie

    Apr 20, 2023 at 5:34 PM

    Very yummy. It’s one of my new favorites! I didn’t change anything, except I did not add chocolate chips to a few muffins and sprinkled with sugar instead.

    Reply
    • Avatar photoSammi (Cotter Crunch Test Kitchen)

      Apr 21, 2023 at 10:35 AM

      Thanks for trying them, Julie! Love that you sprinkled some of the tops with sugar. Great idea!

      Reply
  3. Avatar photoOmnia

    Sep 03, 2022 at 7:23 AM

    Hi. I can’t eat oats, so can I replace it with another flour?

    Reply
    • Avatar photoLindsay Cotter

      Sep 03, 2022 at 2:21 PM

      Hi omnia! I have tried it with all almond flour and the taste is great but it’s a little more dense. That’s the only difference. Can you have almond flour? If so I can send the amount I tried it with.

      Reply
      • Avatar photoOmnia

        Sep 03, 2022 at 3:00 PM

        Thanks Lindsay for getting back to me. Yes I can have almond flour and coconut flour too. It would be great if you could share with me the amount of almond flour you used.

        Thanks again

        Reply
        • Avatar photoLindsay Cotter

          Sep 04, 2022 at 3:58 PM

          So I basically made this almond flour banana muffin https://www.cottercrunch.com/toasted-coconut-banana-muffins-paleo/ but swapped out the coconut for zucchini and added chocolate chips. The only difference was texture but taste was very similar to these with oat flour. Does that make sense?

          Reply
          • Avatar photoOmnia

            Sep 04, 2022 at 4:04 PM

            Yeah sounds great. Will give it a try:) thanks again so much

          • Avatar photoLindsay Cotter

            Sep 04, 2022 at 8:26 PM

            Keep me posted!

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A stack of 3 gluten and dairy-free zucchini muffins with a text overlay for pinterest.
Lindsay Cotter of Cotter Crunch

About Lindsay

Hi, y’all, I’m Lindsay Cotter, a Nutrition Specialist with a focus on Gluten-Free eating. I love creating delicious nourishing food that anyone can enjoy.

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A stack of 3 gluten and dairy-free zucchini muffins with a text overlay for pinterest.

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A stack of 3 gluten and dairy-free zucchini muffins with a text overlay for pinterest.
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