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    Gluten Free Chocolate Zucchini Muffins

    Modified: Apr 4, 2026 · 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 what happens when you have a big pile of garden zucchini and a serious chocolate craving at the same time and I have to tell you the result is absolutely incredible. They are rich, fudgy, and packed with double chocolate flavor from cocoa powder and a full cup of semi-sweet chocolate chips and every single bite is so decadent that nobody ever believes there is a vegetable hiding inside.

    The zucchini completely disappears into the batter and what you are left with is the most moist and perfectly tender chocolate muffin you have ever pulled out of your oven.

    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

    I love making a batch of these at the start of the week because they are perfect for grabbing on busy mornings, packing in lunchboxes, or enjoying as an afternoon treat with a cup of coffee.

    They freeze beautifully which makes them one of my favorite gluten free meal prep recipes for summer.

    If you grow zucchini you are going to want to make these immediately and if you do not you are going to want to find a neighbor who does.

    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
    • Storage
    • 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 together.

    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 rich, fudgy, and packed with double chocolate flavor from cocoa powder and semi-sweet chocolate chips that makes every single bite completely irresistible. Fresh grated zucchini keeps every muffin incredibly moist and tender and the deep chocolate flavor means nobody will ever guess there is a vegetable hiding inside. Naturally gluten free, ready in just 45 minutes, and the most delicious way to use up summer garden zucchini all season long!


    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 together.

    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: American

    Did you make this recipe?

    Tag @smallfarmbiglife on Instagram and hashtag it #smallfarmbiglife

    If you made these Gluten Free Chocolate Zucchini Muffins I would love to hear what you thought! Please leave a star rating and a comment below. These are one of my favorite summer baking recipes and I hope they become a staple in your kitchen too!

    Storage

    Store these gluten free chocolate zucchini muffins in an airtight container at room temperature for up to 3 days. If the weather is hot store them in the refrigerator for up to 5 days. These muffins also freeze exceptionally well! Place cooled muffins in a freezer safe bag or container and freeze for up to 3 months. Thaw at room temperature or microwave for 20 to 30 seconds for a quick and delicious chocolate treat straight from the freezer.

    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 before grating it for these muffins?

    You do not need to peel the zucchini before grating it. The skin is thin and soft and completely disappears into the dark chocolate batter so you will never see or taste it. If you are trying to hide the zucchini from picky eaters the deep chocolate color of the batter already makes it virtually impossible to detect so peeling is entirely optional.

    Do I need to squeeze the moisture out of the zucchini before adding it to the batter?

    No and I actually recommend against it. The moisture in the fresh grated zucchini is exactly what makes these chocolate zucchini muffins so incredibly moist and fudgy in every bite. Simply grate the zucchini on the large side of a box grater, measure out two cups, and add it directly to the batter. The zucchini will release its moisture as the muffins bake and that is what gives you that perfect soft and tender chocolate muffin texture.

    Can I use dark chocolate chips instead of semi-sweet?

    Absolutely and I actually love the result with dark chocolate chips. Dark chocolate gives these muffins an even richer and more intense chocolate flavor that pairs beautifully with the cocoa powder in the batter. You can also use milk chocolate chips if you prefer a sweeter muffin or use a combination of both. Any type of chocolate chip works well in this recipe.

    More Gluten Free Recipes

    • Gluten Free Strawberry Upside Down Cake
    • Cheesy Cauliflower Casserole
    • High Protein Cottage Cheese Dip
    • Air Fryer Teriyaki Chicken Thighs

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