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    Home » Recipes » Gluten Free Muffins & Scones

    Gluten Free Zucchini Chocolate Chip Muffins

    Published: Sep 15, 2025 by Nicole Spiridakis

    Jump to Recipe Print Recipe

    Tuck shredded squash into these gluten free zucchini chocolate chip muffins for a delectable morning treat. Fluffy, chocolatey, delicious!

    Interior views of gluten free zucchini chocolate chip muffins.

    This chocolate-y version of my gluten free zucchini muffins recipe adds, you guessed it, chocolate chips (I also like to stir in some walnuts for extra nutty flavor and crunch when I have them). A mix of my homemade gluten free flour blend and almond flour creates a sturdy yet moist muffin that bursts with threads of fresh, shredded zucchini. Easy to keep dairy-free if needed, these are anything but basic!

    Jump to:
    • Yes, Please Add Chocolate Chips!
    • Ingredients Needed
    • How to Make Zucchini Chocolate Chip Muffins
    • Baking Tip: Add Chocolate On Top
    • Tips & Variation Ideas
    • Proper Storage
    • More Gluten Free Zucchini Recipes
    • Recipe

    Yes, Please Add Chocolate Chips!

    I'm a fan of adding chocolate to just about everything, and it's hard to go wrong when swirling little bites of semisweet goodness into muffins. Not as rich, of course, as a gluten free chocolate zucchini cake, these veg-heavy muffins can almost count as breakfast. But don't worry -- they're still sweet enough to taste like a treat. Here's why I love these gf muffins:

    • The easiest. No mixer needed her - just a whisk and a spoon, meaning you'll have the batter ready to go fast without any fuss.
    • Simple ingredients. (Gluten free) flour, baking powder, spice, eggs ... you know, the basics you need for almost any baking recipe. I love the accessible ingredients list for this one!
    • That hit of chocolate. I already loved my gluten free zucchini muffins and when I throw in a handful of melty chocolate chips? It makes them even better.
    Ingredients for gluten free zucchini chocolate chip muffins are text-labeled.

    Ingredients Needed

    Here's a look at what you need for this recipe. Make sure to scroll down to my recipe card at the bottom of this post for the full ingredient amounts and instructions.

    • Gluten free flour - Use a preferred 1:1 gluten-free all-purpose flour blend.
    • Almond flour - I love using fine-ground almond flour in muffins and quick breads for structure and moisture.
    • Granulated sugar - Feel free to swap light brown sugar for a deeper flavor note.
    • Baking powder
    • Cinnamon - Or a spice blend such as pumpkin pie or apple pie spice mix.
    • Salt - Use fine sea salt or table salt.
    • Eggs - Large or medium eggs are fine.
    • Milk - Any milk, including whole, 2%, or dairy-free milk, is great.
    • Oil - A neutral oil, such as vegetable, canola, or avocado oil, works well, and I've also had success with melted coconut oil and olive oil.
    • Zucchini - No need to peel the zucchini, but do give it a squeeze before adding to the batter.
    • Chocolate chips - I love semisweet chocolate chips, and milk chocolate is also nice.
    A plate of gluten free zucchini chocolate chip muffins and a cup of coffee plus a solo muffin.

    How to Make Zucchini Chocolate Chip Muffins

    Here's an overview in photos of how to make these sweet muffins:

    Flours are mixed together to make gluten free zucchini chocolate chip muffins.

    1. Mix dry ingredients: In a large bowl, whisk together the dry ingredients.

    Eggs and oil are whisked in a bowl.

    2. Combine wet ingredients: In a separate bowl, mix together the wet ingredients.

    The batter for gluten free zucchini chocolate chip muffins in a bowl.

    3. Put it together: Mix the wet ingredients into the dry mix until smooth.

    Zucchini is stirred into gluten free muffin batter.

    4. Add zucchini and chocolate: Now stir in the shredded zucchini and chocolate chips.

    Muffin batter in a muffin tin.

    5. Rest batter: Portion out the muffin batter into a greased muffin tin and rest the batter for 15 minutes.

    A batch of gluten free zucchini chocolate chip muffins cool in a tin.

    6. Bake: Place in a 400°F oven and bake for about 20 minutes.

    Baking Tip: Add Chocolate On Top

    If I have some mini chocolate chips, I love sprinkling them over the tops of the muffins before I pop the tin into the oven. In a pinch, I use regular chocolate chips, just a tad less of them. This is a fun, optional step to add a bit of extra chocolate to each muffin.

    A pretty napkin next to gluten free zucchini chocolate chip muffins and coffee.

    Tips & Variation Ideas

    • How to grate the zucchini? Like many other recipes that call for zucchini, you won't need to peel the zucchini before adding it to the batter. Just give it a wash, trim the ends, and grate. I use the large grate on my box grater for these muffins to give them a bit of texture, but you can also do a finer grate.
    • Squeeze the zucchini - To prevent the muffins from getting too soggy, squeeze the shredded zucchini to remove as much water as possible. I just squeeze it between my (clean!) hands.
    • Rest the batter - Let the batter rest while the oven heats, or for at least 15 minutes to hydrate the gluten free flours.
    • Fill the muffin cups ⅔ full for this recipe - In this particular recipe, I've found that about ⅔ full is the sweet spot so that they rise nicely but don't overflow each muffin cup.
    • Add nuts - For extra crunch, add ½ cup chopped walnuts or pecans.
    • Refined sugar-free - Swap maple syrup or coconut sugar for the granulated sugar.
    • Reduce the sugar - I like a sweet muffin, what can I say? However, if you like your muffins slightly less sweet, use ½ cup of sugar rather than ¾ cup of sugar.
    • Dairy-free - Swap out the milk for dairy-free milk, or in a pinch, use water.
    • Make whole grain muffins - Use your favorite whole grain gluten free flour, such as oat flour, sorghum flour, or brown rice flour, instead of the gluten-free all-purpose flour by weight.
    A gluten free zucchini chocolate chip muffin cut in a half on a plate and a cup of coffee.

    Proper Storage

    Make sure to cool fresh muffins thoroughly before placing them in an airtight container for storage; they may get soggy if they're added while still warm.

    • Counter - Place the fully cooled muffins in an airtight container and store them on the counter for up to 3 days. Make sure the muffins are thoroughly cooled before placing them in the storage container so that they don't get soggy.
    • Fridge - Keep the muffins in an airtight container in the fridge for up to 5 days.
    • Freezer - Store the muffins in a freezer-safe bag with as much air removed as possible for up to 3 months in the freezer. Thaw the muffins completely in the fridge before eating them.

    More Gluten Free Zucchini Recipes

    • A pile of gluten free banana zucchini muffins on a plate.
      Gluten Free Banana Zucchini Muffins
    • Squares of gluten zucchini chocolate cake.
      Gluten Free Zucchini Chocolate Cake
    • A loaf of gluten-free zucchini bread on a board with a plate and a slice and a cup of tea.
      Gluten-Free Zucchini Bread
    • A sliced loaf of gluten free banana & zucchini bread with a slice on a plate.
      Gluten Free Banana & Zucchini Bread

    Happy baking! If you make this recipe, I'd love to know. Please leave a comment below, reach out with any questions, and tag me on Instagram @Cucina Nicolina  ❤️

    Recipe

    A pretty napkin next to gluten free zucchini chocolate chip muffins and coffee.
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    Gluten Free Zucchini Chocolate Chip Muffins

    Nicole Spiridakis
    Tuck shredded squash into these gluten free zucchini chocolate chip muffins for a delectable morning treat.
    5 from 1 vote
    Print Recipe Pin Recipe
    Prep Time 10 minutes mins
    Cook Time 25 minutes mins
    Total Time 35 minutes mins
    Course Breakfast
    Cuisine American
    Servings 12 servings
    Calories 262 kcal

    Ingredients
     
     

    • 1 ½ cups gluten free flour (180 grams)
    • ½ cup almond flour (60 grams)
    • ¾ cup granulated sugar
    • 1 tablespoon baking powder
    • 1 teaspoon fine sea salt
    • 1 teaspoon ground cinnamon
    • 2 large eggs
    • ½ cup whole milk or dairy-free milk
    • ⅓ cup vegetable oil
    • 1 cup zucchini shredded, packed
    • ¾ cup semisweet chocolate chips

    Instructions
     

    • Preheat your oven to 400°F. Grease a 12-well muffin pan.
    • In a large bowl, whisk together the 1 ½ cups gluten free flour , ½ cup almond flour, ¾ cup granulated sugar, 1 tablespoon baking powder, 1 teaspoon fine sea salt, and 1 teaspoon ground cinnamon.
    • In a small bowl, whisk together the 2 large eggs, ½ cup whole milk and ⅓ cup vegetable oil.
    • Make a well in the center of the dry ingredients and pour in the wet ingredients, stirring gently to combine. Fold in the 1 cup zucchini and ¾ cup semisweet chocolate chips, then divide the batter equally between the muffin wells. Let the batter rest for 15 minutes.
    • Place in the oven and bake for about 20-25 minutes, until the muffins are lightly browned and a tester comes out clean. Cool in the pan set on a rack for 10 minutes, then turn out to cool completely.

    Notes

    CN's Tips
     
    • How to grate the zucchini? Like many other recipes that call for zucchini, you won't need to peel the zucchini before adding it to the batter. Just give it a wash, trim the ends, and grate. I use the large grate on my box grater for these muffins to give them a bit of texture, but you can also do a finer grate.
    • Squeeze the zucchini - To prevent the muffins from getting too soggy, squeeze the shredded zucchini to remove as much water as possible. I just squeeze it between my (clean!) hands.
    • Rest the batter - Let the batter rest while the oven heats, or for at least 15 minutes to hydrate the gluten free flours.
    • Fill the muffin cups ⅔ full for this recipe - In this particular recipe, I've found that about ⅔ full is the sweet spot so that they rise nicely but don't overflow each muffin cup.
    • Refined sugar-free - Swap maple syrup or coconut sugar for the granulated sugar.
    • Reduce the sugar - I like a sweet muffin, what can I say? However, if you like your muffins slightly less sweet, use ½ cup of sugar rather than ¾ cup of sugar.
    • Dairy-free - Swap out the milk for dairy-free milk, or in a pinch, use water.
    • Make whole grain muffins - Use your favorite whole grain gluten free flour, such as oat flour, sorghum flour, or brown rice flour, instead of the gluten-free all-purpose flour by weight.

    Nutrition

    Serving: 1 muffinCalories: 262kcalCarbohydrates: 32gProtein: 4gFat: 14gSaturated Fat: 4gPolyunsaturated Fat: 4gMonounsaturated Fat: 3gTrans Fat: 0.05gCholesterol: 34mgSodium: 307mgPotassium: 110mgFiber: 3gSugar: 18gVitamin A: 87IUVitamin C: 2mgCalcium: 105mgIron: 2mg
    Disclaimer: Nutrition information is automatically calculated and is an estimate (I'm not a nutritionist and can't guarantee accuracy!). Even when not specified, be sure to check that all the ingredients you use are gluten free if you need them to be by reading labels on all packaging and/or confirming with the manufacturer.
    Did you make this recipe?Let me know in the comments how it went!

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      Gluten Free Maple Pumpkin Muffins
    5 from 1 vote (1 rating without comment)

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    Welcome!

    Cucina Nicolina is your home for carefully tested gluten-free baking recipes made with simple, wholesome ingredients. I'm a writer, recipe developer, and cookbook author who loves to share all things yummy and gluten-free. Learn more about me.


    The cover of the cookbook Flourless: Recipes for Naturally Gluten-Free Desserts by Nicole Spiridakis shows an opera cake.

    My cookbook, Flourless, was published by Chronicle Books and is full of naturally gluten-free desserts to tempt everyone! Learn more.

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