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    Home » Recipes » Breakfast

    Gluten-free Pumpkin Chocolate Chip Muffins (paleo, dairy free)

    Modified: Feb 15, 2025 • Published: Sep 6, 2022 by Dr. Erin Carter • This post may contain affiliate links • 4 Comments

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    These are the best gluten-free pumpkin chocolate chip muffins! They are so easy to make and these delicious muffins are also dairy free, nut free and paleo, but they are so good that you would never know it! They are the perfect fall breakfast or snack.

    Gluten free pumpkin muffins with chocolate drizzled over them on a baking rack.

    Fall means it's time for all things pumpkin including paleo pumpkin chocolate chip cookies, edible pumpkin cookie dough, gluten free chocolate chip cookie bars and the delicious pumpkin muffin recipe I am sharing with you today!

    Table of Contents
    • Why you will love this recipe:
    • Ingredients and substitutions:
    • Recipe variations and add ins:
    • How to make gluten-free pumpkin chocolate chip muffins:
    • Top tips:
    • How to store:
    • Gluten-free pumpkin chocolate chip muffins FAQs:
    • Other gluten-free muffin recipes you will love:
    • Recipe

    Why you will love this recipe:

    • These healthy pumpkin chocolate chip muffins have the best flavour with hints of cinnamon and maple syrup. They do not have a strong pumpkin flavour, so even if you don't like pumpkin you will still love them.
    • These pumpkin muffins are surprisingly quick and easy to make and since they are made in one bowl the clean up is so simple.
    • Besides being gluten-free these muffins are also dairy-free, nut free, grain free, refined sugar free, and paleo, just like my healthy chocolate avocado muffins.
    • They make a great breakfast, snack or healthy treat, just like my gluten-free chocolate chip zucchini muffins and gluten-free orange chocolate chip muffins.
    • These paleo pumpkin muffins freeze really well and are perfect for meal prep. 

    Want an even easier pumpkin treat? Make pumpkin mousse or pumpkin Rice Krispie treats instead.

    Ingredients and substitutions:

    • Tapioca Flour - this is also known as tapioca starch and is used to give these muffins the most light and fluffy texture. Note that tapioca flour and cassava flour are not the same thing, so don't confuse the two. 
    • Coconut Flour - when combined with the tapioca flour these gluten-free flours blend perfectly to give these pumpkin muffins the perfect texture. 
    • Spices: ground cinnamon, nutmeg, cloves, allspice and sea salt - this combination of spices gives these muffins that perfect fall flavour. 
    • Baking soda - to help these muffins rise when they bake and get that perfect light and fluffy texture. Don't try using baking powder.
    • Pumpkin puree - you can either make your own or use canned pumpkin puree. This is to add the delicious pumpkin flavour and more moisture to these muffins. Just don't use pumpkin pie filling as it's too sweet. 
    • Coconut milk- to add more moisture and a nice sweet flavour to the muffins. I recommend using full fat coconut milk for the best taste. You could swap this for another dairy free milk or even dairy milk if you tolerate dairy. 
    • Maple syrup - one of my favourite natural sweeteners that adds a delicious richness and depth to these muffins while keeping them refined sugar free.
    • Coconut oil - to add moisture and help these gluten-free pumpkin chocolate chip muffins get that perfect crumbly texture when they bake. 
    • Eggs - a key ingredient to help these muffins rise. I have not tried using any egg replacers for this recipe and do not recommend it. This is not a vegan pumpkin muffin recipe. 
    • Vanilla extract - to help enhance the delicious fall flavours of these muffins. 
    • Chocolate chips - I like using dark chocolate chips to make these muffins but you can use any type of chocolate chips that you prefer. To keep the muffins refined sugar free use chocolate chips sweetened with coconut sugar.

    Recipe variations and add ins:

    • For more texture add some chopped nuts such as pecans or walnuts. 
    • You could add a chocolate drizzle like I did for the photos by melting a dark chocolate bar with 1 tablespoon of coconut oil and then drizzling it over the cooked muffins.

    How to make gluten-free pumpkin chocolate chip muffins:

    A large bowl filled with muffin batter.
    1. Step 1: First, preheat your oven to 350 degrees Fahrenheit and line a muffin tray with parchment paper muffin cups. While the oven is heating, add all the ingredients, except the chocolate chips, into the bowl of your standing mixer and blend well until the batter is smooth.
    A large bowl with muffin batter in it with chocolate chips on the batter.
    1. Step 2: Stir in the chocolate chips by hand.
    1. Step 3: Then transfer the batter to the muffin cups, and fill each cup until level with the tray. Bake for 30-35 minutes, until a toothpick inserted inside comes out clean.
    A baking rack with pumpkin muffins with chocolate drizzle on them.
    1. Step 4: Let the muffins cool, then enjoy!

    Top tips:

    • If you don't have a standing mixer you can mix the ingredients by hand using a whisk or spoon.
    • Don't try swapping the maple syrup for honey. I have tried it and the muffins don't taste as good.
    • Use room temperature eggs for best results. 
    • Let the muffins cool completely before serving.

    How to store:

    Store these muffins in an airtight container in the fridge for up to 7 days. 

    These muffins freeze really well for up to 3 months in a freezer safe bag or container so feel free to make a double or triple batch and save more for later. 

    A gluten free pumpkin muffin with chocolate drizzle on it, on a baking rack with other muffins.

    Gluten-free pumpkin chocolate chip muffins FAQs:

    Can I use cassava flour instead of tapioca flour?

    No! Cassava flour and tapioca flour are very different flours. Cassava flour requires way more liquid ingredients to bake properly so if you tried using it these muffins would turn out very very dry.

    What can I use instead of coconut flour?

    I do not recommend trying to swap the coconut flour for another flour. These muffins won't turn out.

    Can I use pumpkin pie filling instead of pumpkin puree?

    I do not recommend it. Pumpkin pie filling is already sweetened and flavours with spices so it would change the taste of these muffins completely. 

    Are these muffins vegan?

    Despite being dairy free these pumpkin muffins are not vegan because they contain eggs. I do not recommend trying to omit the eggs from this recipe to make these muffins vegan. I don’t think they will turn out as coconut flour requires eggs to bake and rise properly. 

    Is canned pumpkin the same as pumpkin puree?

    Yes! Canned pumpkin (not pumpkin pie filling) is just cooked pumpkin that has been pureed. 

    Other gluten-free muffin recipes you will love:

    • A muffin pan filled with a batch of baked blueberry muffins.
      Paleo Blueberry Muffins (gluten-free & dairy-free)
    • A batch of chocolate avocado muffins on a baking rack with cut up avocado beside them.
      The Best Chocolate Avocado Muffins (gluten-free, dairy free)
    • A batch of banana pecan muffins on a baking rack topped with a pecan streusel topping.
      Gluten-Free Banana Pecan Muffins
    • A batch of banana protein chocolate chip muffins on a baking rack.
      Banana Protein Muffins (easy, healthy & gluten-free)

    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 baking rack with pumpkin muffins with chocolate drizzle on them.

    Gluten-Free Pumpkin Chocolate Chip Muffins

    These gluten-free pumpkin chocolate chip muffins are so good! Easy to make they have the most amazing flavour and are the perfect healthy breakfast or snack.
    5 from 8 votes
    Print Pin Rate
    Course: Breakfast, Dessert, Snack
    Cuisine: American
    Diet: Gluten Free, Low Lactose
    Prep Time: 10 minutes minutes
    Cook Time: 30 minutes minutes
    Total Time: 40 minutes minutes
    Servings: 12 muffins
    Calories: 216kcal
    Author: Dr. Erin Carter

    Equipment

    • standing mixer
    • Muffin pan
    • Parchment paper muffin cups

    Ingredients

    Muffin Ingredients

    • 1 cup coconut flour
    • 1/2 cup tapioca flour
    • 1 tablespoon ground cinnamon
    • 1 teaspoon ground nutmeg
    • 1 teaspoon baking soda
    • 1/4 teaspoon ground cloves
    • 1/4 teaspoon ground allspice
    • pinch sea salt
    • 1 cup cooked pumpkin puree (canned or homemade)
    • 3/4 cup full fat coconut milk
    • 1/3 cup maple syrup
    • 1/4 cup coconut oil, melted
    • 1 tablespoon organic vanilla extract
    • 4 large eggs (preferably organic and free range)
    • 1 cup dark chocolate chips

    Instructions

    Muffin Instructions

    • Preheat your oven to 350F.
    • Line a muffin tray with parchment paper muffin liners.
    • Add all the ingredients for the muffins, except for the chocolate chips, into the bowl of your standing mixer.
    • Blend well on low until the ingredients are smooth.
    • Stir the chocolate chips in by hand.
    • Transfer the batter to the muffin cups, and fill each cup until level with the tray.
    • Place the tray in the oven and bake for 30-35 minutes, until a toothpick inserted into a muffin comes out clean.
    • Serve and enjoy!

    Notes

    1. This recipe yields 12 muffins. 
    2. Allow the muffins to cool before eating.
    3. You can use either canned or homemade pumpkin puree. 
    4. Nutritional values are an estimate and will vary depending on the specific ingredients you use. 

    Nutrition

    Calories: 216kcal | Carbohydrates: 20g | Protein: 4g | Fat: 14g | Saturated Fat: 11g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 1g | Cholesterol: 55mg | Sodium: 138mg | Potassium: 137mg | Fiber: 5g | Sugar: 8g | Vitamin A: 3260IU | Vitamin C: 1mg | Calcium: 35mg | 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. Mary

      October 03, 2020 at 9:43 pm

      Can I use egg substitute?

      Reply
      • Erin Carter

        October 04, 2020 at 2:00 pm

        Hey Mary! I've never tried the recipe with an egg substitute. Typically cassava flour needs eggs in order to bake properly but if you do decide to give it a try please let us know how it goes.

        Reply
    2. Joanne

      October 08, 2019 at 1:54 am

      These muffins look delicious! I don't use tapioca flour; can almond flour be used instead?

      Reply
      • Erin Carter

        October 12, 2019 at 4:53 pm

        Hey Joanne!
        So tapioca flour and almond flour are very different. I wouldn't recommend trying to sub almond for tapioca. I don't think it will work out.

        Reply

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    My name is Dr. Erin Carter and I am so thrilled you are here. I am a physician with specialties in both internal medicine and rheumatology, and I believe that food and healthy living are forms of medicine. In my spare time I share health information and delicious, healthy recipes here on Pure and Simple Nourishment.

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