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    Home » Recipes » Breakfast

    Gluten-Free Chocolate Chip Zucchini Muffins (dairy-free & paleo)

    Modified: Mar 6, 2025 • Published: Aug 20, 2020 by Dr. Erin Carter • This post may contain affiliate links • 3 Comments

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    These are the best gluten-free chocolate chip zucchini muffins! Not only do they taste amazing but they are really easy to make and these healthy muffins are made with almond flour and are also dairy-free, paleo, and refined sugar free.

    A chocolate chip zucchini muffin with a bite out of it and chocolate pieces around it.

    Healthy muffins like my gluten-free banana chocolate chip muffins, chocolate avocado muffins and gluten-free lemon blueberry muffins are some of my favourite recipes to create, and I've made another delicious healthy muffin recipe that I can't wait for you to try!

    Table of Contents
    • Why you will love this recipe:
    • Ingredients and substitutions:
    • Recipe variations and add ins:
    • How to make gluten-free chocolate chip zucchini muffins:
    • Top Tips:
    • Gluten-free chocolate chip zucchini muffins FAQs:
    • Other gluten-free baked goods you will love:
    • Recipe

    Why you will love this recipe:

    • The taste! These are the absolute best gluten-free zucchini muffins! They have the most amazing firm muffin tops yet are nice and moist on the inside.
    • Even though they are made from scratch they are really easy to make and you don't have to squeeze the liquid out of the zucchini, making them even easier!
    • These muffins freeze really well so they are great for meal prep, just like my orange chocolate chip muffins.
    • They are made in one bowl so the clean up is quick and easy. 
    • Besides being gluten-free, these healthy zucchini muffins are also grain-free, paleo, dairy-free and refined sugar free. 

    If you love baking with zucchini you will also love my healthy double chocolate zucchini bread!

    Ingredients and substitutions:

    For the full ingredient list and exact measurements refer to the recipe card later in this post.

    Jump to the Recipe Card.
    The ingredients needed to make chocolate chip zucchini muffins separated into bowls including flour, shredded zucchini, coconut sugar, eggs and baking soda.
    • Almond flour - One of my favourite gluten-free flours that gives these muffins the most amazing flavour. Be sure to use almond flour and not almond meal which is more gritty. You could also swap this for cashew flour. 
    • Tapioca flour or tapioca starch – this helps give the muffins such a light and fluffy texture.
    • Coconut flour – this helps add just the perfect amount of crunch to the muffin top. I don't recommend swapping this for another flour. 
    • Coconut sugar – My favourite natural granulated sugar that adds the perfect amount of sweetness to these muffins while keeping them refined sugar free.
    • Full fat coconut milk - to add even more moisture to these delicious muffins. You could swap this for another milk such as almond milk or cashew milk.
    • Eggs - these help the muffins rise when they bake and help the muffins stay together. I have not tried making these muffins without eggs or with any egg replacements and am not sure if any swaps would work.
    • Coconut oil - this helps add moisture to these muffins.
    • Fresh zucchini - the star of these muffins! This adds tons of moisture to these muffins plus a nice serving of veggies.
    • Dark chocolate chips - Instead of chocolate chips you can also use chocolate chunks or broken chocolate bars.

    Recipe variations and add ins:

    • These muffins freeze really well so feel free to make a double or triple batch and save some for later.
    • Feel free to add other additions such as raisins or chopped nuts. 
    • Instead of chocolate chips you can use chocolate chunks or broken chocolate bars.

    How to make gluten-free chocolate chip zucchini muffins:

    A stainless steel bowl filled with egg yolks, grated zucchini, coconut sugar and flour.
    1. Step 1: Preheat your oven to 350 degrees Fahrenheit and add all the ingredients, except the chocolate chips to the bowl of your standing mixer.
    A stainless steel bowl filled with batter.
    1. Step 2: Blend the ingredients until you have a smooth batter.
    A stainless steel bowl filled with a chocolate chip batter.
    1. Step 3: Stir in the chocolate chips by hand.
    A muffin tray with chocolate chip muffin batter in each muffin cup.
    1. Step 4: Line a muffin tray with parchment paper muffin cups and fill each muffin cup with the batter. Bake the muffins for 25 minutes, until a toothpick inserted inside comes out clean.

    Top Tips:

    • Do not try swapping the flours! I have not tested this recipe with any other flour combinations and don't suspect they will work out if you make your own substitutions.
    • I always recommend lining your muffin tray with parchment paper muffin liners. This ensures your food will not come into contact with the non-stick coating on the tray and helps make your clean up even easier.
    • You do not need to squeeze the liquid out of the zucchini before making these muffins.
    • To keep these muffins refined sugar free use chocolate chips sweetened with coconut sugar.
    A stack of three chocolate chip zucchini muffins, the top one with a bite out of it showing chunks of chocolate.

    Gluten-free chocolate chip zucchini muffins FAQs:

    Can I use cassava flour instead of tapioca flour?

    No! They will not turn out. Cassava flour and tapioca flour are totally different flours and cannot be used interchangeably.

    Is there a substitute for almond flour?

    If you can't have almond flour I would recommend cashew flour instead.

    Can I omit the eggs or use an egg replacement?

    I have not tested this recipe without eggs myself, but have had a few readers try both chia seed and flax seed eggs with success.

    How should I store these muffins?

    Store these muffins in an airtight container in the fridge for up to 7 days. These muffins also freeze really well in an airtight bag or container for up to 3 months.

    Other gluten-free baked goods you will love:

    • A muffin pan filled with a batch of baked blueberry muffins.
      Paleo Blueberry Muffins (gluten-free & dairy-free)
    • Pieces of chocolate chip banana bread stacked on top of each other.
      Healthy No Added Sugar Banana Bread - gluten-free & dairy-free
    • A plate with many pieces of cornbread on it, one of them with a slab of butter on top with a drizzle of honey on it.
      Gluten-Free Cornbread with Almond Flour (moist & fluffy)
    • A batch of almond flour biscuits in a basket lined with a blue striped tea towel.
      Easy Almond Flour Biscuits (gluten-free, dairy-free & paleo)

    Since you made it this far we are basically best friends so be sure to follow me on Instagram, Pinterest, TikTok and Facebook where I share even more recipes and healthy living tips! And don’t forget to leave this recipe a star review before you go!

    Recipe

    A paleo chocolate chip zucchini muffin with a bite out of it.

    Gluten-free Chocolate Chip Zucchini Muffins

    These are the best gluten-free chocolate chip zucchini muffins. They are so easy to make and are also dairy free and paleo.
    5 from 10 votes
    Print Pin Rate
    Course: Breakfast, Snack
    Cuisine: American
    Diet: Gluten Free, Low Lactose
    Prep Time: 10 minutes minutes
    Cook Time: 25 minutes minutes
    Total Time: 35 minutes minutes
    Servings: 12
    Calories: 279kcal
    Author: Dr. Erin Carter

    Equipment

    • standing mixer
    • Muffin pan
    • Parchment paper muffin cups

    Ingredients

    • 2 1/2 cups almond flour
    • 1/2 cup tapioca flour
    • 1/2 cup coconut sugar
    • 2 tablespoon coconut flour
    • 1 teaspoon baking soda
    • pinch sea salt
    • 3 large eggs
    • 1 cup grated zucchini
    • 1/2 cup full fat coconut milk
    • 1/4 cup melted coconut oil
    • 1 teaspoon organic vanilla extract
    • 1 cup chocolate chips

    Instructions

    • Preheat your oven to 350F.
    • Add all the ingredients, except for the chocolate chips, to the bowl of your standing mixture and blend everything well until you have a smooth batter.
    • Stir in the chocolate chips by hand.
    • Line a muffin tray with large parchment paper muffin cups and fill each cup with batter until it is full, and slightly heaping.
    • Place the tray in the oven and bake for 25 minutes, until the muffins are golden brown and a toothpick inserted inside comes out clean.
    • Let them cool and enjoy!

    Notes

    1. This recipe yields 12 muffins.
    2. Do not try swapping flours, this recipe has not been tested with any other grain or gluten-free flours and I cannot guarantee that any swaps would work.
    3. Nutritional values are an estimate and will vary depending on the specific ingredients used.  

    Nutrition

    Calories: 279kcal | Carbohydrates: 19g | Protein: 7g | Fat: 21g | Saturated Fat: 8g | Cholesterol: 41mg | Sodium: 139mg | Potassium: 96mg | Fiber: 3g | Sugar: 7g | Vitamin A: 80IU | Vitamin C: 2mg | Calcium: 62mg | Iron: 2mg
    Tried this Recipe? Pin it for Later!Mention @pureandsimpleno or tag #pureandsimpleno!

    DISCLAIMERS: The statements made on this website have not been approved by the Food and Drug Administration or Health Canada. The information is not intended to diagnose, treat, cure, or prevent disease. You assume full responsibility for how you use this information. Always consult with your physician or other health professionals before making any diet or lifestyle changes. This post may contain affiliate links whereby if you purchase these products I receive a small percentage of the sale price. This allows me to keep the blog running and I thank you for allowing me to do that!

    Reader Interactions

    Comments

    1. Lori

      July 30, 2023 at 7:25 pm

      My husband loved these; which is great!! I love that you don’t need to squeeze the zuchinni!! Thank you! Great texture, moistness. I did t add enough chocolate chips, but that was still ok!!5 stars

      Reply
      • Erin Carter

        September 07, 2023 at 8:24 am

        I'm so glad you liked them!

        Reply
    2. Kristie

      August 20, 2020 at 4:39 pm

      Such a delicious treat!5 stars

      Reply

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