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    Home » Recipes » Gluten Free

    Gluten Free Chocolate Chip Muffins

    Published: Nov 23, 2023 · Modified: Aug 26, 2024 by Nicole Addison · This post may contain affiliate links · 9 Comments

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    These gluten free chocolate chip muffins that are made with almond flour and Greek yogurt for a soft and moist crumb. You wouldn't even believe there's no gluten!

    Two halves of a gluten free chocolate chip muffin topped with butter.

    Have you ever bought or made a gluten free baked good that was dry, crumbly, and dissolved into sawdust in your mouth? I have. It wasn't a good time.

    Whether you have Celiac disease or prefer gluten free foods, I'm determined to only deliver the best gluten free recipes that are just as good as their regular counterparts. If you're new here, I've covered pretty much everything from sugar cookies to lemon ricotta pancakes!

    These gluten free chocolate chip muffins are soft, moist and loaded with melty chocolate chips in every bite. They remind me of the mini chocolate chip muffins of my childhood and are amazing for breakfasts, snacks or even adding to your child's lunch.

    Why This Recipe Is Dietitian Approved

    1. Heart healthy. These muffins are made with almond flour that adds heart-healthy unsaturated fats. Canada's dietary guidelines recommends including unsaturated fats in your diet, especially if they replace saturated fats. I also used Greek yogurt to decrease the amount of butter used.
    2. Completely gluten free. We need more gluten free recipes that actually taste good, and these chocolate chip muffins turn out every single time.
    3. Easy snack or breakfast. Muffins are a classic meal prep because they're so easy to whip up a big batch. Pro-tip: make a double batch and freeze half for later!

    Ingredients

    Ingredients including almond flour, chocolate chips, baking powder, baking soda, maple syrup, apple cider vinegar, cinnamon, salt, butter, Greek yogurt.

    Almond flour. Almond flour (different from almond meal) is made by grinding almonds into a fine powder that creates a nice moist baked good. It can be fairly expensive so I highly recommend purchasing it in a large bag like this if you can for the best deal. You can also find it at Costco! I love almond flour gluten free muffins for the soft crumb and healthy fats. 

    Baking soda and baking powder. Yes, BOTH are used in this recipe! Almond flour is lower in carbs so it's much harder to make rise than regular all purpose flour. We need both baking soda and baking powder to help give these muffins some rise! Always check to make sure these are not expired for best results.

    Spices. Cinnamon and salt are all you will need.

    Eggs. I use two whole eggs in this recipe to help provide structure and hold the muffins together. You could use flax eggs, however the muffins will not have the same rise.

    Maple syrup. For a touch of natural sweetness! I recommend using natural maple syrup rather than pancake syrup for the best flavour. Alternatively, swap for honey.

    Greek yogurt. Making gluten free muffins with yogurt helps reduce the saturated fat content by replacing some of the butter while keeping moisture. I use using 2% plain Greek yogurt.

    Apple cider vinegar. Adding an acid such as apple cider vinegar helps activate the leavening agents (baking powder/soda) to create fluffiness! This can be replaced with lemon juice.

    Melted butter. Let's be honest, butter has the best flavor in baked goods. You can also use olive oil or any other neutral tasting oil.

    Chocolate chips. Milk chocolate, semi sweet or dark chocolate all work!

    The complete ingredient list with measurements can be found in the recipe card below. 

    Instructions

    Preheat the oven to 350F and line a 12 cavity muffin tin. 

    Whisking eggs, maple syrup, greek yogurt, apple cider vinegar and melted butter until smooth.

    In a mixing bowl whisk together eggs, maple syrup, Greek yogurt, apple cider vinegar and melted butter until smooth. 

    Mixing in almond flour, baking soda, cinnamon and salt.

    To the same bowl, mix in almond flour, baking soda, baking powder, cinnamon and salt. Stir well. 

    Adding chocolate chips to muffin batter.

    Add in chocolate chips (leaving some to add to the tops of the muffins). 

    Mixing chocolate chip muffin batter.

    Stir the batter until just combined.

    Adding chocolate chip muffin batter into a liner muffin tray.

     Scoop batter into each cavity of the muffin tin (adding about 3 tablespoon of batter into each cavity). Top with additional chocolate chips. Bake for about 22-27 minutes.

    Tray of baked gluten free chocolate chip muffins.

     The muffins are done when the tops and golden brown and a toothpick inserted into the center of the muffin comes out clean.

    Substitutions and Variations

    To make gluten-free: This recipe is naturally gluten free.

    To make dairy-free: I have not tested a dairy-free version, but you could swap the butter for vegan butter, coconut oil or another neutral oil. Be sure to use a dairy-free yogurt and dairy-free chocolate chips.

    To make vegan: For a vegan muffin, try my double chocolate banana muffins or zucchini muffins.

    To make nut-free: For a nut-free and gluten-free muffin, try my oat flour gingerbread muffin recipe.

    Make this recipe your own by switching up the mix-ins! Try white chocolate chips, blueberries or chopped nuts.

    Equipment

    • Mixing bowls
    • Silicone muffin tin (for easy removal)
    • Silicone muffin liners (or regular muffin liners)

    Storage

    The gluten free chocolate chip muffins can be stored in the fridge for up to 5 days in an airtight container. To freeze, wrap them individually and store in an airtight freezer bag. 

    Top Tip

     Use silicone muffin liners or a silicone muffin pan to avoid the muffin batter stick to the pan. This also helps make cleaning a breeze!

    When measuring your flour, be sure to sift the flour into the bowl. Don't pack it into measuring cups as this will overestimate the flour needed and result in a denser, drier muffin.

    Frequently Asked Questions

    Can you make gluten free muffins with oat flour?

    I have before! These pumpkin oat flour muffins are a good recipe to try.

    How to get gluten free muffins to try?

    The trick is to use fresh baking powder & baking soda with an acid (lemon juice or vinegar). This allows for the best rise possible!

    Are gluten free muffins keto?

    As a dietitian I don't recommend the keto diet for the general healthy population. With that being said, these muffins are made with almond flour that is higher in fat and lower in carbs. These aren't sugar free, so they may not fit in your keto diet.

    Are these chocolate chip muffins a balanced breakfast?

    They're a great source of healthy fats and some carbs but I would recommend pairing with a protein source like egg bites.

    Plate of gluten free chocolate chip muffins.

    More Healthy Muffin Recipes

    If you enjoyed these gluten free chocolate chip muffins, here are some more you might like!

    • Protein French Toast Muffins
    • Vegan Zucchini Breakfast Muffins
    • Oat Flour Pumpkin Muffins
    • Banana Blueberry Oatmeal Muffins

    PS. I love seeing my recipes in action! If you decide to make these gluten-free chocolate chip muffins, don't forget to snap a photo and tag me on Instagram- @nourishedbynic or leave a comment and rating below letting me know how you liked it!

    📖 Recipe

    Gluten free chocolate chip muffin with a bite.
    Print Recipe Pin Recipe
    5 from 3 votes

    Gluten Free Chocolate Chip Muffins

    These gluten free chocolate chip muffins that are made with almond flour and Greek yogurt for a soft and moist crumb. You wouldn't even believe there's no gluten!
    Prep Time10 minutes mins
    Cook Time25 minutes mins
    Total Time35 minutes mins
    Course: Breakfast, Dessert, Snack
    Cuisine: American
    Keyword: Breakfast, loaves and muffins
    Servings: 12 muffins

    Ingredients 

    • 2 eggs
    • ⅓ cup + 2 tablespoon maple syrup
    • ¼ cup plain 2% greek yogurt
    • 1 tablespoon apple cider vinegar
    • 2 tablespoon butter melted
    • 2 cups almond flour
    • ½ teaspoon baking soda
    • 1.5 teaspoon baking powder
    • ½ teaspoon cinnamon
    • ½ teaspoon salt
    • ¾ cup chocolate chips

    Instructions

    • Preheat the oven to 350F and line a 12 cavity muffin tin.
    • In a mixing bowl whisk together eggs, maple syrup, Greek yogurt, apple cider vinegar and melted butter until smooth.
    • To the same bowl, mix in almond flour, baking soda, baking powder, cinnamon and salt. Stir well.
    • Mix in chocolate chips (leaving some to add to the tops of the muffins).
    • Scoop batter into each cavity of the muffin tin (adding about 3 tablespoon of batter into each cavity). Top with additional chocolate chips. Bake for about 22-27 minutes. The muffins are done when the tops and golden brown and a toothpick inserted into the center of the muffin comes out clean.

    Notes

    *I have included an estimation of the nutrition information for this recipe below. However, always remember a recipe is so much more than just nutritional content and these numbers do not need to dictate your food choices. Please don't forget that both your body and soul need nourishment! The owner of this website is not liable for this estimation.

    Nutrition

    Serving: 1muffin | Calories: 226kcal | Carbohydrates: 20g | Protein: 5g | Fat: 15g | Saturated Fat: 4g | Polyunsaturated Fat: 0.2g | Monounsaturated Fat: 1g | Trans Fat: 0.1g | Cholesterol: 33mg | Sodium: 224mg | Potassium: 72mg | Fiber: 2g | Sugar: 15g | Vitamin A: 101IU | Vitamin C: 0.003mg | Calcium: 101mg | Iron: 1mg
    Did you know....rating and sharing recipes is one of the best ways you can support your favourite food bloggers? If you make this recipe, I would love if you clicked the stars below to leave a rating and/or sharing a photo on social media by tagging @nourishedbynic or using the hashtag #nourishedbynic!

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    Comments

    1. Michelle Genrich says

      January 23, 2026 at 1:53 am

      5 stars
      Awesome recipe! I substituted the butter for coconut oil and used less maple syrup. Very happy with the texture and flavour. An absolute hit with the kids! Thank you!

      Reply
    2. James Kidner says

      November 24, 2025 at 5:19 am

      These were better than you said. These tookm my breath away to Blondis.

      Reply
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    Nicole Addison, RD

    Hi I'm Nicole!

    I’m a Registered Dietitian, recipe developer and content creator on a mission to help individuals rediscover the joys of cooking with easy, accessible, healthy recipes.

    On my page you'll find yummy recipes, wellness tips, and even some of my favourite travel and lifestyle recommendations!

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