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Published: Aug 1, 2026 by beneficialbento · This post may contain affiliate links · Leave a Comment

Gluten Free Dark Chocolate Zucchini Muffins

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

Dark chocolate zucchini muffin and glass of milk

  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.

chocolate zucchini muffin on plate

Jump to:
  • Notes from Kristie's Kitchen
  • Here's What You Need
  • How to Shred Zucchini
  • My Favorite Tools for Shredding Zucchini
  • How to Make Gluten Free Zucchini Muffins - Step by Step
  • Learn More About Gluten Free Baking
  • Gluten Free Dark Chocolate Zucchini Muffins
  • How to Store and Freeze Gluten Free Muffins
  • What to Eat with Dark Chocolate Zucchini Muffins
  • More Recipes that Use Garden Veggies
  • 💬 Comments

Notes from Kristie's Kitchen

Kristie Winget, creator of Beneficial Bento

I' ve been making these muffins for the past 5 years as one way to use up zucchini from the garden. I make several batches of these muffins during the summer and store them in the freezer. It's so nice to pull a bag of these big bakery style muffins out for a special treat for breakfast or dessert. And they taste amazing frosted with cream cheese frosting!

  • Feeds: This recipe makes a dozen large, bakery style muffins, or up to 18 standard sized muffins.
  • Prep time/ actual time spent in kitchen: about 30 minutes
  • Cooking time:  20-25 minutes
  • A great way to make these muffins extra fudgy and rich is to use dark cocoa powder. I use Hershey's Special Dark cocoa powder for an incredibly over-the-top chocolate flavor. You can use regular cocoa powder if you don't have dark cocoa powder.
zucchini muffin ingredients

Here's What You Need

  • Eggs - I use large eggs in this muffin recipe
  • Nonfat Greek yogurt - when you're baking gluten free, it really helps muffins to bake up light and moist when you  add ingredients that contain as many grams of protein as possible. Including dairy is an easy way to achieve this.
  • Sugar -regular white sugar works here. I like to use natural evaporated cane sugar if possible because it's less processed.
  • Zucchini - the reason for this recipe! Shredding the zucchini on a cheese grater is the best way to incorporate this vegetable into baked goods, like with my gluten free zucchini bread.
  • Brown rice flour blend - this is my own flour blend. Check out the Notes in the recipe card to see how to make it.
  • Coconut flour -I love baking with coconut flour! It smells so sweet and fragrant. It's perfect for sweet baked goods that need to be gluten free.
  • Unsweetened cocoa powder - for these muffins, I prefer using Hershey's Special Dark cocoa powder.
  • Baking powder, baking soda, salt, vanilla - just the standard stuff
  • Xanthan gum - an essential for gluten free baked goods
  • Semi sweet chocolate chips - milk chocolate can be used  but they are so light colored that they look a little out of place in these muffins!
chocolate zucchini muffin with ingredients

How to Shred Zucchini

If you need to shred some zucchini for just one recipe, this box grater is non-slip and sturdy.

If you're going to shred a lot of zucchini, because it's summer and you have so much coming out of your garden that it's getting hard to manage… 😅 it will save you a lot of time if you use a food processor, or this KitchenAid shredder attachment.

My Favorite Tools for Shredding Zucchini

box grater

box grater

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Image of food processor

food processor

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KitchenAid shredder

KitchenAid shredder

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how to shred zucchini

Bonus Tip 👇

Grate the zucchini on the short, cut side instead of the long side. You want the zucchini as small and unobtrusive as possible. No one wants to find long strands of zucchini in their muffins!

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

chocolate zucchini muffins on rack

How to Make Gluten Free Zucchini Muffins - Step by Step

Baking these muffins is really easy! You can use either a stand mixer or a hand mixer. Scroll down to the recipe card for the full recipe and notes.

step 1. add liquids to mixer

Step 1. Combine eggs, yogurt, sugar, and vanilla in a mixer and blend until smooth.

step 2. add zucchini

Step 2.Add the shredded zucchini and blend until evenly combined.

step 3. combine dry ingredients

Step 3. Stir together all the dry ingredients with a whisk, then add in the chocolate chips.

step 4. add dry to wet

Step 4. Add the dry ingredient mixture to the liquids in the mixer a little at a time while the mixer is on low speed. 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.

step 5. cover, let rest

Step 5.Cover the  bowl with a towel and let the batter rest, at room temperature, for at least 15-20 minutes or up to an hour. 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.

step 6. prepare muffin tins

Step 6. Line a muffin tin with paper liners or silicone. I like to use silicone spritzed with a little oil so the muffins slip right out.

step 7. scoop muffin batter

Step 7. Mound the batter in the muffin cups. It will be thick, like brownie batter. A large cookie scoop will give you nice rounded muffin tops. Preheat the oven to 350℉ and bake for 20 - 25 minutes, or until a toothpick inserted in the center comes out clean.

step 8. bake

Step 8. Let cool in the muffin pan for 5 minutes before taking them out. Gluten free baked goods are fragile when hot.

Learn More About Gluten Free Baking

Let's say you baked these delicious dark chocolate zucchini muffins, they were as good as you'd hoped, and now you want to know what else you can make that's gluten free and delicious. I've got you covered, and it's FREEEEE:

get Gluten Free Baking for Beginners free ebook
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Gluten Free Dark Chocolate Zucchini Muffins

chocolate zucchini muffin with ingredients
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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
  • 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 below
  • 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. In a separate bowl, stir all the dry ingredients with a whisk. Add the chocolate chips to the dry flour mixture and stir to combine.
  4. Add the dry ingredient mixture to the liquids in the mixer a little at a time while the mixer is on low speed. 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.
  5. Cover the  bowl with a towel and let the batter rest, at room temperature, for 1at least 5-20 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. When the resting time is almost up, preheat the oven to 350℉.
  6. 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.
  7. Mound the batter in the muffin tins as shown - pile it right up to the top. It will be thick like brownie batter. I  like to use a cookie scoop for this to make it nice and rounded on top. Bake at 350℉  for 20-25 minutes, or until a toothpick or knife inserted in the center comes out clean.
  8. Cool for at least 5 minutes before removing from the muffin tins so the gluten free starches can solidify and set. 

    Gluten free baked goods are fragile when hot.

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.

How to Store and Freeze Gluten Free Muffins

Every summer when I have way too much zucchini I make several batches of these muffins and store them in the freezer. These muffins freeze really well!

freezing gluten free zucchini muffins
  1. Make sure the muffins are completely cooled before freezing them. This will prevent ice crystals from forming, which might make them wet when you thaw them out.
  2. Add them to a freezer bag, or a study container with a lid that's safe for freezing. 
  3. To be extra safe, place the muffins in a freezer bag and then inside a plastic container before freezing. The freezer bag will protect from freezer burn, and the container will keep gluten free baked goods from getting smashed to crumbs.

Remember: gluten free baked goods often get hard and crumbly when they are right out of the refrigerator, but warming them for 20-30 seconds in a microwave will make them soft and fresh again.

What to Eat with Dark Chocolate Zucchini Muffins

Banana bread + pumpkin chocolate chip cookies + white chocolate macadamia nut cookies+ these dk. chocolate zucchini muffins = delicious gluten free dessert tray for a potluck or party

Dk. chocolate zucchini muffin + egg mug = chocolate lover's breakfast (but still healthy)

Dk. chocolate zucchini muffins + zucchini bread + zucchini lasagna = freezer worthy gluten free/zucchini binge baking sesh 😁

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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.

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