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    Gluten Free Chocolate Zucchini Muffins

    Modified: Aug 9, 2025 · Published: Aug 9, 2025 by smallfarmbiglife · This post may contain affiliate links · Leave a Comment

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    These gluten free chocolate zucchini muffins are the ultimate blend of rich, decadent chocolate and wholesome zucchini, creating a moist, tender bite every time. With a double chocolate punch from cocoa and chocolate chips, these easy chocolate zucchini muffins taste like an indulgent dessert while secretly packing in hidden veggies.

    They're a homemade sweet you can whip up from scratch in no time. They are great for a quick breakfast, an afternoon snack, or a satisfying treat for your sweet tooth. The grated zucchini melts seamlessly into the batter, ensuring each bite stays soft and fudgy without a trace of veggie texture.

    a white plate with three gluten free chocolate zucchini muffins on it next to the muffin pan of muffins and a muffin that has been broken in half to show it's fluffy center

    Whether you call them GF Chocolate Zucchini Muffins, Double Chocolate Zucchini Muffins, or simply the best chocolate zucchini muffins you've ever had, this recipe delivers.

    It's a yummy treat that proves baked goods with zucchini can be every bit as decadent as your favorite chocolate desserts. With their rich cocoa flavor, bursts of chocolate chips, and bakery-style texture, these gluten free muffins are the perfect way to enjoy an indulgent yet secretly wholesome snack.

    One bite and you'll see why this zucchini baking recipe is a go-to for chocolate lovers.

    You might also like my Easy Gluten Free Zucchini Brownies, my Gluten Free Zucchini Chocolate Chip Cookies, my Gluten Free Zucchini Bread or my Gluten Free Zucchini Muffins.

    You can find all of my dessert recipes here: Gluten Free Dessert Recipes

    a white plate with four gluten free zucchini muffins on it with one broken in half
    Jump to:
    • Ingredients
    • Instructions
    • Supplies
    • More Recipes You Might Enjoy
    • Gluten Free Chocolate Zucchini Muffins
    • Top Tip
    • Frequently Asked Questions

    Ingredients

    • Granulated Sugar
    • Brown Sugar
    • Avocado Oil or Vegetable Oil
    • Eggs
    • Vanilla Extract
    • Gluten Free Flour
    • Cocoa Powder
    • Salt
    • Baking Soda
    • Baking Powder
    • Ground Cinnamon
    • Zucchini
    • Semi-Sweet Chocolate Chips

    Instructions

    Preheat your oven to 350 degrees.

    Line 20 muffin pan cups with cupcake liners or grease with coconut oil or butter. Set the pan aside.

    In a large mixing bowl whisk together the gluten free flour, cocoa powder, salt, baking soda, baking powder and cinnamon. Set aside.

    In the bowl of your stand mixer add the sugar, brown sugar, oil, eggs and vanilla. Beat until a smooth batter forms. Add the dry ingredients and blend just until mixed togther.

    Add the grated zucchini to the mixture and blend just until incorporated. Add the chocolate chips and blend just until they are mixed in.

    Remove the bowl from your stand mixer and using a spatula scrape the sides and make sure all the ingredients from the bottom are mixed in.

    Using a cookie scoop or spoon put the batter into the muffin pan. The batter should be slightly below the top of the cupcake liner or muffin tin cup for 20 muffins.

    Bake at 350 degrees for 25-30 minutes.

    When you take the muffins out of the oven test the center with a toothpick. The toothpick should come out clean. If it doesn't bake the muffins another 3-5 minutes until a toothpick inserted in the center comes out clean.

    Supplies


    More Recipes You Might Enjoy

    • Easy Gluten Free Zucchini Brownies
    • Gluten Free Zucchini Chocolate Chip Cookies
    • Gluten Free Zucchini Muffins
    • Gluten Free Zucchini Bread

    I get a lot of my ingredients from Thrive Market. Thrive Market has been a game changer for me eating gluten free. They have so many options I can't get at my rural grocery stores! Use this link to get 40% off your first order!

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    Gluten Free Chocolate Zucchini Muffins


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    • Author: Elaine VanVleck
    • Total Time: 45 minutes
    • Yield: 20 1x
    • Diet: Gluten Free
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    Description

    These gluten free chocolate zucchini muffins are the ultimate blend of rich, decadent chocolate and wholesome zucchini, creating a moist, tender bite every time. With a double chocolate punch from cocoa and chocolate chips, these easy chocolate zucchini muffins taste like an indulgent dessert while secretly packing in hidden veggies. 


    Ingredients

    Units Scale
    • 1 cup Granulated Sugar
    • ½ cup Brown Sugar
    • ¾ cup Avocado Oil or Vegetable Oil
    • 3 large Eggs
    • 2 tsp Vanilla Extract
    • 2 ½ cups Gluten Free Flour
    • ½ cup Cocoa Powder
    • 1 tsp Salt
    • 1 tsp Baking Soda
    • 1 tsp Baking Powder
    • 1 tsp Ground Cinnamon
    • 2 cups Grated Zucchini
    • 1 cup Semi-Sweet Chocolate Chips

    Instructions

    Preheat your oven to 350 degrees.

    Line 20 muffin pan cups with cupcake liners or grease with coconut oil or butter. Set the pan aside.

    In a large mixing bowl whisk together the gluten free flour, cocoa powder, salt, baking soda, baking powder and cinnamon. Set aside.

    In the bowl of your stand mixer add the sugar, brown sugar, oil, eggs and vanilla. Beat until a smooth batter forms. Add the dry ingredients and blend just until mixed togther.

    Add the grated zucchini to the mixture and blend just until incorporated. Add the chocolate chips and blend just until they are mixed in.

    Remove the bowl from your stand mixer and using a spatula scrape the sides and make sure all the ingredients from the bottom are mixed in.

    Using a cookie scoop or spoon put the batter into the muffin pan. The batter should be slightly below the top of the cupcake liner or muffin tin cup for 20 muffins.

    Bake at 350 degrees for 25-30 minutes.

    When you take the muffins out of the oven test the center with a toothpick. The toothpick should come out clean. If it doesn't bake the muffins another 3-5 minutes until a toothpick inserted in the center comes out clean.

    • Prep Time: 15 minutes
    • Cook Time: 30 minutes
    • Category: Breakfast, Snacks
    • Method: Baking
    • Cuisine: Gluten Free

    Did you make this recipe?

    Tag @smallfarmbiglife on Instagram and hashtag it #smallfarmbiglife

    Top Tip

    A medium size zucchini usually makes 4 cups of grated. I like to make these muffins using 2 cups and then make my gluten free zucchini bread recipe using the other 2 cups and put that in the oven when these come out.

    Frequently Asked Questions

    What is the best gluten free flour to use for muffins?

    My favorite gluten free flours for baking are King Arthur Measure for Measure Gluten Free Flour and Bob's Redmill Gluten Free 1-to-1 Baking Flour. I've had really good success using these two flours in my recipes.

    Should I peel the zucchini for muffins?

    You don't need to peel zucchini for muffins. However, if you are hiding the zucchini in the muffin for a picky eater peeling it makes it really hard to see in the muffins.

    More Gluten Free Recipes

    • Gluten Free Blueberry Coffee Cake
    • Gluten Free Chocolate Sourdough Bread
    • Gluten Free Valentine's Day Recipes
    • Gluten Free Frog Eye Salad

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