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Modified: Nov 1, 2025 · Published: Aug 25, 2021 by beneficialbento · This post may contain affiliate links ·

Gluten Free Dark Chocolate Zucchini Muffins

This post contains affiliate links. Thank you for supporting Beneficial Bento!

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  Do you have a never ending supply of zucchini from your garden, and you're getting just a little tired of cranking out zucchini noodles? I have come up with a rich, chocolatey treat that will disguise the zucchini, and it's gluten free too.

 My recipe for Gluten Free Dark Chocolate Zucchini Muffins will use up that  zucchini, and I promise you won't get tired of eating these! If you have a lot of excess zucchini from your garden, this is one of the yummiest ways to turn it into something delicious.

Dark chocolate zucchini muffin and glass of milk

See how I make this recipe

Here's how easy and delicious it is to add zucchini (and chocolate) to your life:

Print

Gluten Free Dark Chocolate Zucchini Muffins

Dark chocolate zucchini muffin and glass of milk
Print Recipe

These gluten free dark chocolate zucchini muffins are one of the most delicious ways to add zucchini (and chocolate) to your life!

They are rich, chocolatey, gluten free, and (even though no one would ever guess)  they are also full of zucchini! If you have a lot of excess zucchini from your garden, this is one of the yummiest ways to turn it into something delicious.

  • Author: beneficialbento
  • Prep Time: 30
  • Cook Time: 25
  • Total Time: 55 minutes
  • Yield: 18 muffins 1x
  • Category: dessert
  • Method: bake
  • Diet: Gluten Free

Ingredients

Scale
  • In mixer:
  • 4 large eggs, or 1 cup of egg
  • 1 cup nonfat, Greek yogurt
  • 1 cup sugar
  • 2 teaspoons vanilla
  • 3 cups finely shredded zucchini - grate on the short end, not the long end!
  • Dry ingredients:
  • 1 ½ cups (210g) of my Brown Rice Flour Blend *see Notes
  • ½ cup (60g) coconut flour
  • 1 cup (90g)unsweetened cocoa powder ( my favorite: Hershey's Special Dark)
  • 1 ½ teaspoons baking soda
  • 1 teaspoon baking powder
  • 2 teaspoons xanthan gum
  • ½ teaspoon salt
  • 1 cup semi sweet chocolate chips

Instructions

  1. Combine eggs, yogurt, sugar, and vanilla in a mixer and blend until smooth.
  2. Add the shredded zucchini and blend until evenly combined.
  3. Sift all the dry ingredients, minus the chocolate chips.
  4. Add the chocolate chips to the dry flour mixture and stir to combine.
  5. Add the dry ingredient mixture to the liquids in the mixer a little at a time while the mixer is on low speed.
  6. Turn up the speed to medium and blend for 1 -2 minutes. Don't skip this step - it will really hydrate the gluten free flours, making the finished muffins really moist.
  7. Cover the  bowl with a towel and let the batter rest, at room temperature, for 15-20 minutes. This is another step toward fully hydrating the flours - gluten free flours absorb liquids unevenly (and more slowly) so this step will help get you those moist, rich, muffins you see in the photos.
  8. When the resting time is almost up, preheat the oven to 350℉.
  9. Fill a muffin tin with paper or silicone liners. When I use silicone liners, I like to give each one a spritz with cooking spray to make clean-up easier.
  10. Mound the batter in the muffin tins as shown. You can fill it more full than with regular (wheat based) muffin recipes. I like to use a cookie scoop for this to make it nice and rounded on top.
  11. Bake at 350℉  for 25 minutes.
  12. Cool for at least 5 minutes before removing from the muffin tins so the gluten free starches can solidify and set.
  13. Store extras, covered, in the fridge. Gluten free baked goods often turn a little hard and crumbly when they're cold, but will re-heat beautifully in the microwave. Try a few seconds to a half a minute per muffin.

Notes

My Brown Rice flour Blend is basically 3  parts brown rice flour + 1 part tapioca starch + 1 part potato starch. You will see this in a lot of my gluten free recipes, and it's one of the flour blends you can find in my free PDF, Gluten Free Baking for Beginners.

Nutrition

  • Serving Size: 1 muffin
  • Calories: 235
  • Sugar: 23.1 g
  • Sodium: 204.7 mg
  • Fat: 7.8 g
  • Carbohydrates: 39.2 g
  • Fiber: 4.8 g
  • Protein: 6.7 g

We all love a good sugary treat now and then, but if you need a break and want to cut carbs and calories - here's a collection of our favorite sugar free recipes: Delicious Easy Recipes for Sugar Free Meals.

 What's in your Brown Rice Flour Blend?

 Basically, it's 3  parts brown rice flour + 1 part tapioca starch + 1 part potato starch. You will see this in a lot of my gluten free recipes, and it's one of the flour blends you can find in my free PDF, Gluten Free Baking for Beginners

 I don't want to see long strings of zucchini when I'm eating a chocolate muffin - yuck!


 You won't notice it if you grate it on the short end, or the cut side of the zucchini (as shown in the video). Small shreds of zucchini just bake right into the muffins and mostly dissolve. If you see any zucchini at all, it will just look like a little bit of shredded coconut.

Can I skip resting the batter for 20 minutes?

If you do, the muffins might be kind of dry or have a gritty, grainy texture. Gluten free recipes almost always use a combo of several kinds of flour, and they all absorb the liquids in a recipe at different rates. Resting the batter will allow all the flour to fully absorb the liquids, giving you really moist and fudgy muffins. For more gluten free baking tips, be sure to read "Best Beginner's Tips for Successful Gluten Free Baking"

 Can I rest the batter for longer, like an hour or two?

If you cover it and put it in the fridge, an hour would probably be alright. But if you wait too much longer than that, the baking powder and baking soda will start to lose their potency and your muffins might not rise very high.

Can I substitute full-fat Greek yogurt for the non-fat kind?

Yes, and the results are delicious! But keep in mind - it will change the nutrition stats. I used non-fat Greek yogurt to reduce the calories a bit.

Can I substitute a non-calorie sweetener for the sugar?

You could replace the sugar with an equal portion of zero calorie granular sweetener. I have used  monk fruit/erythritol blend with good results, but the muffins were a little more dry than when I  made them with sugar.

Can you eat zucchini skin?

Yes. The skin contains the healthy carotenoids, so you don't want to peel it off. The skin is very thin anyway so why bother?

What are the health benefits of eating zucchini?

High fiber, low calories. Fiber can help with G I digestive issues, which is common for gluten free people. Contains a high mount of manganese, vitamin A, potassium, magnesium, Vitamin C.

Get Gluten Free Baking for Beginners to get the Brown Rice flour blend instructions, gluten free biscuit mix recipe, and simple recipes and information for the gluten free beginning baker.

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Hey there! My name's Kristie and I'm glad you're here :)

I'm a gluten free recipe creator, cookbook contributor, and YouTube creator. I love teaching how you can have fun with your food in spite of food allergies or special diets. Bento box lunches are what got me started, and gluten free baking is my specialty.

More about me →

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