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Home > Recipes > Meal type > Muffins, Cupcakes & Donuts
Gluten Free Chocolate Zucchini Muffin sitting on a plate.

Small Batch Gluten Free Chocolate Zucchini Muffins

  • DF
  • GF

No ratings yet
Prep Time 15 minutes mins
Cook Time 30 minutes mins
Total Time 45 minutes mins
Whether you have a zucchini in the fridge that needs to be used up or you are trying to sneak some extra vegetables into your fussy eater then I have the recipe for you! These gluten free chocolate zucchini muffins are moist (thanks to the zucchini), chocolatey and taste so, so delicious! 
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11 March 2026
March 11, 2026

by

Sarah Bell

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These healthier chocolate muffins are made using wholesome ingredients like almond flour, buckwheat flour, coconut sugar and, of course, zucchini. They are filled with healthy fats, protein and fibre to provide more sustained energy and less of a sugar spike (while still being delicious!). They are also dairy-free as I use olive oil instead of butter, which contributes to the moist crumb. 

Baked gluten free chocolate zucchini muffins in a muffin tin.
Contents:
  1. Everything You Need to Make Gluten-Free Chocolate Zucchini Muffins
  2. How to Make Zucchini Double Chocolate Muffins
  3. Storage 
  4. Gluten Free Chocolate Zucchini Muffins

Looking for more ways to use up extra zucchini? Then try my Gluten Free Savoury Zucchini Slice or these Turkey and Zucchini Meatballs. 

Looking for more recipes to sneak extra veggies into your fussy eater? Then try this Gluten Free Chocolate Chip Pumpkin Bread or this Hidden Veggie Beef Mince Pasta Bake.

Everything You Need to Make Gluten-Free Chocolate Zucchini Muffins

I’ve listed all of the ingredients that you will need below including any possible substitutions or ingredient notes. The ingredient quantities can be found in the recipe card at the bottom of this post. 

Wet Ingredients

  • zucchini – this recipe calls for a medium sized zucchini, equal to around 175 grams. I recommend finely grating the zucchini as it helps the zucchini to really disappear into the crumb (my pickiest eater didn’t even notice the muffins had zucchini in them!). 
  • large eggs 
  • soy milk – you can use your choice of milk like cow’s milk or almond milk. 
  • extra virgin olive oil – you can swap for macadamia oil or avocado oil. I wouldn’t recommend swapping for coconut oil as the muffins will harden up much more when refrigerated. 

Dry Ingredients

  • sea salt flakes 
  • almond flour – also known as bleached almond meal. I love using almond flour as it adds moisture to a gluten-free bake while also providing healthy fats and protein. 
  • coconut sugar – I love using coconut sugar as a natural alternative, however if you don’t have any then you can try swapping the coconut sugar for brown sugar. It will bake a little differently but it should work. 
  • buckwheat flour – buckwheat flour is a really healthy gluten free flour to use. It is a great source of minerals and fibre. This recipe only requires a small amount so there is no obvious buckwheat flavour. 
  • tapioca flour – tapioca flour helps to lighten up the almond flour. Gluten-free baking can be really tricky but I find almond flour, buckwheat flour and tapioca flour are the perfect blend of gluten-free flours. 
  • cacao powder – you can swap cacao powder for cocoa powder. I prefer cacao powder as it has more antioxidants and is less processed. 
  • baking powder – choose a gluten free baking powder if you are gluten intolerant of coeliac. Make sure you use baking powder and not baking soda. 
  • dark chocolate chips – choose good quality dark chocolate chips. 
Ingredients for gluten free chocolate zucchini muffins laid out in individual bowls.

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How to Make Zucchini Double Chocolate Muffins

These muffins are really easy to make, only taking around 15 minutes to prep. First, preheat the oven to 180°C/356°F (conventional). Line a 12 hole muffin tin with 9 muffin liners or cupcake liners. 

Once you have finely grated the zucchini, you need to squeeze out the excess moisture. I like to do this by placing the grated/shredded zucchini into a nut milk bag or cheese cloth and holding it over the sink. Squeeze out the excess liquid and then transfer to a large mixing bowl. 

Add the eggs, milk, olive oil and a pinch of salt to the bowl and whisk to combine. Next add the almond flour and coconut sugar to the egg mixture. Sift in the buckwheat flour, tapioca flour, cacao powder and baking powder. Stir well to combine until you have a smooth batter. Pour the chocolate chips into the bowl and stir until just combined.

Wet ingredients for gluten free chocolate zucchini muffins mixed together in a bowl.
Dry ingredients added to wet ingredients to make gluten free chocolate zucchini muffins.
Chocolate chips added to  muffin batter in a bowl.
Gluten free chocolate zucchini muffins batter in a bowl.

Divide the batter evenly between the muffin liners using a spoon or ice cream scoop. Use a spatula to get every last bit of batter out of the bowl. Place the muffin pan into the oven on the middle shelf. Bake for 30 minutes or until a skewer inserted comes out with no batter (there will be some melted chocolate from the choc chips). 

Gluten free chocolate zucchini muffins, uncooked in a baking tray.
Baked gluten free chocolate zucchini muffins.

Once baked, remove from the oven and transfer the muffins to a wire rack to cool. These muffins are best enjoyed warm or room temperature. 

Gluten Free Chocolate Zucchini Muffin sitting on a plate.

Storage 

 In warmer climates, store the muffins in an airtight container in the fridge for up to 4 days. Or store in the freezer for up to 3 months. To give them that just baked feel, pop a muffin into the microwave for 20-30 seconds before enjoying.

Gluten Free Chocolate Zucchini Muffins

No ratings yet
By: Sarah Bell
Whether you have a zucchini in the fridge that needs to be used up or you are trying to sneak some extra vegetables into your fussy eater then I have the recipe for you! These gluten free chocolate zucchini muffins are moist (thanks to the zucchini), chocolatey and taste so, so delicious! 
Baked gluten free chocolate zucchini muffins in a muffin tin.
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Prep Time 15 minutes mins
Cook Time 30 minutes mins
Total Time 45 minutes mins
Servings: 9

Equipment

  • Large mixing bowl
  • Measuring Cups and Spoons
  • Box grater
  • Whisk
  • Muffin pan
  • Muffin liners

Ingredients

  • 1 medium zucchini, (175g) finely grated, moisture squeezed out
  • 2 large eggs
  • 1/3 cup extra virgin olive oil
  • 1/3 cup soy milk
  • Pinch sea salt flakes
  • 1 cup almond flour
  • ¾ cup coconut sugar
  • ½ cup buckwheat flour
  • ½ cup tapioca starch
  • 1/3 cup cacao powder
  • 1 ½ teaspoons baking powder
  • 2/3 cup dark chocolate chips
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Instructions 

  1. Preheat the oven to 180°C/356°F (conventional). Line a muffin tin with 9 muffin liners.
  2. To a large bowl add the grated zucchini, eggs, olive oil, soy milk and pinch of salt. Whisk until well combined.
  3. Add the almond flour and coconut sugar to the bowl and sift in the buckwheat flour, tapioca flour, cacao powder and baking powder. Stir until well combined.
  4. Pour the chocolate chips into the bowl and stir until just combined.
  5. Divide the batter between the muffin liners and then place into the oven on the middle shelf. Bake for 30 minutes or until cooked through. Test if they are cooked through by inserting a skewer into the centre of a muffin, if it comes out without cake batter on it then they are done (note that there will be melted chocolate on the skewer from the chocolate chips).
  6. Remove from the oven and cool for 5 minutes before transferring to a wire rack to cool completely. These muffins are best eaten warm or at room temperature.

Notes

Nutrition facts are an estimate only. 

Storage

Store the muffins in the fridge in an airtight container for up to 4 days. Warm in the microwave for 30 seconds to get that just baked feel.

Nutrition

Calories: 332kcalCarbohydrates: 35gProtein: 7gFat: 20gSaturated Fat: 6gPolyunsaturated Fat: 1gMonounsaturated Fat: 7gTrans Fat: 0.004gCholesterol: 41mgSodium: 64mgPotassium: 325mgFiber: 4gSugar: 15gVitamin A: 139IUVitamin C: 5mgCalcium: 124mgIron: 2mg
Course: Dessert,healthy treats,lunchbox,Snack,Sweets
Cuisine: American,Australian
Diet: Gluten Free,Low Lactose
Keyword: gluten free baking,gluten-free muffins,healthy baking,zucchini muffins
Tried this recipe?Post your recreation to Instagram and mention @ournourishingtable or tag #ournourishingtable! Don’t forget to let us know how you went by rating this recipe and commenting below.

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My debut cookbook–Our Nourishing Week

My debut cookbook Our Nourishing Week is a collection of 85+ easy and nutritious recipes for the whole family. It includes 6 weeks of meal plans, complete with shopping lists – simplifying your family meals for an easy, healthy week – every week.

order now

Hi, I’m Sarah!

I’m a nutritionist turned healthy recipe developer who is all about creating delicious food designed to nourish. I love using wholefood ingredients and have a strong focus on gluten free, dairy free and refined sugar free recipes.

MORE ABOUT ME >

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My debut cookbook–Our Nourishing Week

My debut cookbook Our Nourishing Week is a collection of 85+ easy and nutritious recipes for the whole family. It includes 6 weeks of meal plans, complete with shopping lists – simplifying your family meals for an easy, healthy week – every week.

order now

Hi, I’m Sarah!

I’m a nutritionist turned healthy recipe developer who is all about creating delicious food designed to nourish. I love using wholefood ingredients and have a strong focus on gluten free, dairy free and refined sugar free recipes.

MORE ABOUT ME >

Hey there, I’m Sarah!

I’m a Bachelor qualified Nutritionist turned healthy recipe developer and the creator of Our Nourishing Table.

I love creating easy to make, nutrient-filled recipes from quick dinner recipes and make-ahead breakfasts to healthy treats and luscious desserts (with a healthy spin of course).

more about me

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