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Double Chocolate Zucchini Muffins | Vegan & Gluten-Free

by Capri Lilly

These decadent Double Chocolate Zucchini Muffins are packed with double the chocolate and incredible nutrients from the zucchini! These moist chocolatey muffins are vegan, gluten-free, and refined sugar-free giving you a healthy, delicious treat that everyone will love! 

If you love delicious treats packed with nutrients, you’ll definitely want to try my Chocolate Avocado Bread or Zucchini Blueberry Muffins next!


chocolate muffins with vegetables

These Double Chocolate Zucchini Muffins check off the list of all of everything I hope for in my treats! They are:


Refined Sugar-free: perfectly sweetened with maple syrup and coconut sugar!

Gluten-Free: using my favorite All-Purpose Gluten-Free Flour, Bob’s Red Mill 1:1 GF Flour

Vegan: No eggs (or animal byproducts) here! Instead, flax egg and applesauce are used to bind the ingredients together! 

Just a little bit healthier: By adding shredded zucchini, you get the amazing nutritional benefits from the zucchini, including antioxidants, vitamins, and minerals that improve digestion and heart health! The best part is that you cannot taste the zucchini in the muffins one bit AND they help to make these muffins moist and fluffy!

You already know I am a huge fan of gluten-free vegan zucchini muffins. My Blueberry Zucchini Muffins are super popular on the site! What better way to keep the zucchini muffin train going than creating a delicious vegan gluten-free double chocolate chip zucchini muffin recipe!?

What do you need to make these Fluffy Gluten-Free Chocolate Zucchini Muffins

  • Flour: To keep these muffins gluten-free I use Bob’s Red Mill 1:1 GF All-Purpose Flour. If you are not gluten intolerant, you can substitute with regular flour. You’ll also need a bit of almond flour. This helps to make the muffins extra fluffy and absorb any excess moisture. 
  • Zucchini: Using a cheese grater, you can shred the zucchini until you have about 2 cups of shredded zucchini. Usually, I use about 1-2 zucchinis depending on the size.
  • Cocoa Powder: You can use Dutch Processed Cocoa Powder or Raw Cacao Powder. Both options work great in this recipe
  • Flax Egg: Flax Egg is very easy to make. You simply mix 1 tablespoon of ground flax with 2.5 tablespoons of water and let it sit for 10 minutes (this gives you one flax egg). After it thickens, it is ready to use! (To note: For non-vegan option, you can always substitute 1 flax egg for 1 egg)
  • Applesauce: Helps bind the ingredients together and keep the muffins moist
  • Sweetener: Maple syrup and Coconut Sugar. (can sub brown sugar for coconut sugar)
  • Spices and such: Salt, vanilla extract, coconut oil, baking powder, baking soda, apple cider vinegar
baking healthy zucchini muffins at home-2
Double Chocolate Zucchini Muffins Before Baking

How to make zucchini muffins

Making Chocolate Zucchini Muffins is super easy! 

First, you will grate the zucchini until you get 2 cups of shredded zucchini. Then, using a paper towel or cloth squeeze as much moisture out of the zucchini as you can. You should get about ¼ of a cup of liquid after squeezing out the excess moisture.

zucchini with liquid squeezed out

Next, all you do is mix the liquid ingredients together in a medium-sized bowl and mix the dry ingredients together in a separate bowl. Then you will slowly incorporate the dry ingredients into the wet ingredients and mix until the batter is formed.

To Note: The mix should be thick, but spoonable. If there is excess moisture in the mix, add 1 tablespoon of almond flour at a time up 3 tablespoons. If the mixture is too dry, add 1 tablespoon of almond milk at a time up to 3 tablespoons. 

zucchini mixture to make chocolate muffins
how to make chocolate zucchini muffins gluten free healthy

How to Store your Double Chocolate Zucchini Muffins

These healthy chocolate muffins store well if kept in an airtight container and placed in the fridge. You can enjoy these Double Chocolate Zucchini Muffins for up a week! 


Also, if you want to freeze them for a later date, these zucchini muffins freeze extremely well. Simply put them in a freezer-proof bag and they can be stored for up to 2 months. When you are ready to enjoy them, thaw them in the microwave for ~30 seconds or leave them on the countertop. You’ll be happy to see they taste just as great as when you first made them!

the best gluten free chocolate muffins healthy
Double Chocolate Zucchini Muffins Fresh Out of the Oven!

What to eat with these Double Chocolate Zucchini Muffins

These Chocolate Zucchini Muffins are perfect for a sweet treat to start your day! Have one (or two!) for breakfast with your coffee or a smoothie. I also encourage you to save some for dessert! They are the perfect light dessert if you are looking for something to satisfy your chocolate cravings!

Here are some of my favorite smoothies: 

vegan and gluten free muffins with zucchini

I hope you enjoy this Double Chocolate Zucchini Muffin recipe! 

Paired with coffee, it’s the perfect way to start your day, or topped with ice cream, it’s the perfect way to finish it! Don’t forget to connect with me on INSTAGRAM and PINTEREST, for your daily dose of healthy delicious recipes! 

If you make these Double Chocolate Zucchini Muffins, don’t forget to rate the recipe and let me know what you think in the comments below! I love hearing from you!

chocolate homemade glutenfree vegan muffins healthy
Print Recipe
5 from 11 votes

Double Chocolate Zucchini Muffins | Vegan and Gluten-free

These decadent Double Chocolate Zucchini Muffins are packed with double the chocolate and incredible nutrients from the zucchini! These moist chocolatey muffins are vegan, gluten-free, and refined sugar-free giving you a healthy, delicious treat that everyone will love!
Prep Time15 mins
Cook Time25 mins
Total Time40 mins
Course: Breakfast, Dessert, Snack
Cuisine: American, Gluten-Free, Gluten-Free Dessert, Healthy Options, Vegan
Keyword: chocolate, gluten free dessert, gluten free zucchini muffins, gluten-free, good food baddie, goodfoodbaddie, healthy, healthy zucchini muffins recipe, muffins, vegan, vegan zucchini muffins
Servings: 10 muffins
Calories: 166kcal
Author: Capri Lilly


  • 1 1/2 cup All Purpose Gluten-Free Flour (like Bob's Red Mill 1:1 GF Flour)
  • 1 tbsp Ground Flax
  • 2.5 tbsp Water
  • 1 tsp Baking Soda
  • 2 tsp Baking Powder
  • 3 tbsp Coconut Sugar
  • 1/4 tsp Sea Salt
  • 2 cups Grated Zucchini
  • 1 tsp Apple Cider Vinegar
  • 1/4 cup Maple Syrup
  • 1 tsp Vanilla Extract
  • 1/4 cup Coconut Oil, melted
  • 1/4 cup Applesauce
  • 3 tbsp Almond Flour
  • 1/3 cup Cocoa Powder or Raw Cacao Powder
  • 1/3 cup Chocolate Chips (ensure vegan if necessary)


  • Preheat the oven to 350°F. Place muffin liners into a standard, 12-muffin pan. Set aside.
  • Prepare the flax egg: Combine 1 tbsp ground flax with 3 tbsp purified water, mix well, and let sit for 10-15 minutes.
  • Using a grater, shred 2-3 zucchinis until you have 2 cups of shredded zucchini. Set aside.
  • Combine all the dry ingredients (except the almond flour) into a large mixing bowl.
  • Using a paper towel or clean cloth, gently squeeze the liquid from the zucchini. (You should have 1/4 cup liquid drained). In a separate large mixing bowl, combine the liquid ingredients and zucchini and mix well.
  • Slowly add the dry mix to the zucchini mixture. After the ingredients are fully combined, add 1-3 tablespoons of almond meal as needed to absorb any excess moisture.
  • Fold in your choice of mix-ins. Then evenly distribute batter among muffin tins, filling about 3/4 of the way full.
  • Bake for 25-30 minutes or until toothpick inserted into the middle of the muffin comes out clean.
  • Remove from the oven and allow the muffins to cool inside the muffin tin for 10 minutes then remove muffins and transfer to wire rack to finish cooling for 5-10 minutes.


  • Store muffins in an airtight container on the kitchen counter and Enjoy for up to 3 days.
  • Store the muffins in an airtight container and place in the fridge to enjoy for up to a week
  • Muffins can be frozen; individually wrap muffins in ziploc bags or store them in a large freezer bag. Reheat for 30-45 seconds in the microwave or thaw them at room temperature.

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@gristleandgossip September 23, 2020 - 7:26 pm

5 stars
Loved this. We just made fudgy zucchini brownies this past weekend and had some dried zucchini leftover. This recipe couldn’t have come at a better time.

Shani @coinedcuisine September 24, 2020 - 10:58 pm

5 stars
I absolutely love sneaking in veggies into my desserts since I have such a sweet tooth. These muffins were fantastic!

Capri Lilly September 25, 2020 - 2:34 am

Hi Shani! I have a sweet tooth too so I can totally relate! I am glad you like the recipe!

Robin September 25, 2020 - 4:22 am

5 stars
Zucchini bread and chocolate together has long been a favorite of mine. Now that I’m gluten intolerant, I can’t wait to try your recipe. You’re my shero!

Capri Lilly September 28, 2020 - 5:18 pm

:)! I am so happy you like the recipe! This is def one of my all-time favorites 🙂

Chenée Lewis September 28, 2020 - 9:04 pm

5 stars
These muffins were such a hit!! It was a great way to use up some zucchini I had, and they were so moist and delicious!

Samantha September 28, 2020 - 9:57 pm

5 stars
These muffins are so tasty and chocolatey! They are my favorite vegan muffins!

Capri Lilly September 30, 2020 - 11:22 pm

Hi Samantha! I am so happy you like the muffins! 🙂

Kari Alana September 29, 2020 - 2:34 pm

5 stars
This is the perfect way to use up the excess zucchini from my Victory Garden!

Capri Lilly September 30, 2020 - 11:21 pm

Victory Garden!? That sounds magical! I am glad you found a way to use up your zucchini! Hope it was a nice treat 🙂

Mila September 29, 2020 - 2:36 pm

5 stars
I really love the fudgy finish. These were just so decadent, but I love that I got my veggies in too!

Capri Lilly September 30, 2020 - 11:19 pm

Fudge is my middle name! I love a good fudgy chocolatey treat! I am glad you liked the recipe!

Tamara September 29, 2020 - 8:11 pm

5 stars
Wow! These muffins were AMAZING! It was the perfect way to use up some zucchini I had on hand. Also perfect to sneak in the veggies for my kids! They couldn’t even tell the zucchini was in them!

Capri Lilly September 30, 2020 - 11:19 pm

I LOVE sneaking in veggies! The look on the kiddies’ faces when you told them it had zucchini in it was priceless I am sure!

Britney September 30, 2020 - 9:03 pm

5 stars
You always have the best recipes and the fact that they’re healthy always makes it even better!! I love this recipe because it made me feel like I was indulging in a decadent dessert without all of the calories and fats and sugars etc. I love this blog so much! Thanks Capri!

Capri Lilly September 30, 2020 - 11:17 pm

Thank you Britney!! I am so happy to hear you like the recipes! These chocolate muffins are a whole love language for me! Glad you like!

Jazz October 7, 2020 - 2:59 pm

5 stars
Made these muffins and they came out SO fudgy and moist. Couldn’t taste the zucchini at all!

Capri Lilly October 7, 2020 - 4:53 pm

Hi Jazz! Isn’t that the best! The fact that you cant tell there are veggies in your treat! 🙂

Barry J. October 9, 2020 - 4:05 am

I have to be honest, I don’t like zucchini at all. But this may be the only way I’ll eat it! I’ve always heard of how well chocolate and zucchini went well together and you definitely proved it. Thanks for an amazing recipe!

Capri Lilly October 9, 2020 - 10:01 pm

You’re welcome! I am glad you found a new way to enjoy zucchini! With chocolate isn’t bad at all 🙂

Kate October 9, 2020 - 9:51 pm

5 stars
What a delicious way of eating zucchini. Our family loves these muffins.

Capri Lilly October 9, 2020 - 10:02 pm

Hi Kate! I am happy to hear you and your family like the muffins! 🙂

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