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Gluten Free Chocolate Chip Muffins

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These Gluten Free Chocolate Chip Muffins are your answer to a small batch, gluten free, and naturally sweetened bakery style muffin!  This is an easy small batch recipe for 4 tender muffins made with an almond flour blend, perfectly sweetened with coconut sugar, and studded with plenty of chocolate chips.

Close up of a bite taken from a gluten free chocolate chip muffin

Gluten Free Chocolate Chip Muffins

I am slowly starting to test existing recipes on the blog as gluten free and sweetened with more natural sugar.  And I figure what better way to start than with some of the staple baking recipes, like cupcakes and these Gluten Free Chocolate Chip Muffins.

If you happen to be looking for a traditional breakfast muffin recipe, I do have easy recipes for Chocolate Chip Muffins and Chocolate Cherry Muffins – both are made with regular ol’ all purpose flour and granulated sugar.

However, these gluten free chocolate chip muffins offer the same great flavor and texture you come to expect with a bakery-style muffin.

  • Dense – Dense usually isn’t a word you want to associate with baking.  However, in the case of muffins, it is what we are looking for.  Muffins have a higher ratio of dry ingredients to wet which is what gives a traditional muffin it’s ‘heft’ and breakfast-worthy character.  
  • Tender and Moist – Being a more dense baked good, these chocolate chip muffins are still be described as tender and moist.  All of the ingredients work together to make sure the muffins don’t bake up like little cardboard pucks.
  • Balanced Sweetness – A wonderful characteristic (or two) of coconut sugar is that, 1.) it doesn’t taste like coconut, and 2.) it provides a more subtle sweetness to bakes.  Therefore, you aren’t left with a cloyingly sweet muffin, but rather perfectly balanced taste and texture.
  • Lots of Chocolate Chips – You are sure to get a chocolate chip in every bite of these muffins.  Plus, a few extra added on top don’t hurt!

Gluten Free, Dairy Free, Refined Sugar Free Muffins

  1. Gluten Free – The almond flour blend is also considered Paleo, which is great if you are trying to avoid grains.  Which can be found in other gluten free flours.
  2. Dairy Free – The fats found in traditional muffins (butter and sour cream) are replaced with coconut oil and coconut yogurt.
  3. Refined Sugar Free – Coconut sugar is a natural and unrefined sugar.  In baked goods, the flavor is indiscernible.  But make no mistake, it is still sugar.  It just doesn’t go through the same amount of stripping and processing that white table sugar does.  
Gluten free chocolate chip muffins stacked on a wire rack

What You Need To Make Gluten Free Chocolate Chip Muffins

Dry Ingredients

  • Almond Flour
  • Arrowroot Flour
  • Coconut Flour
  • Tapioca Flour
  • Coconut Sugar – There are a few brands of coconut sugar I recommend.  Big Tree (as pictured below), Anthony’s (linked in the recipe – one of my favorites because it comes in a big 5lb bag), and Madhava.  All are great.
  • Baking Powder and Soda – We are using both to make sure the muffins puff up nice and tall.
  • Salt
  • Egg – 1 egg is all we need for this small batch muffin recipe.
  • Coconut Yogurt – I like to use So Delicious unsweetened coconut yogurt and it should be available at your grocery, Target and/or Walmart.  
  • Coconut Oil – The coconut oil is solid and often called cold pressed.  It will need to be melted for about 1 minute.
  • Vinegar – I have tested the recipe using apple cider vinegar and white distilled vinegar.  Both work great.  The vinegar reacts with the baking soda to help give the muffins lift.
  • Chocolate Chips – I like to use semi-sweet chocolate chips, but feel free to use any chocolate chip you like.
  • Turbinado SugarThe turbinado sugar is optional to sprinkle on top and gives the tops of the muffins a little crunch.  You can omit if you are following a (strict) sugar protocol.

Baking Equipment

  • Muffin/Cupcake Pan
  • Cupcake Liners
  • Mixing Bowls

*Paleo/Almond Flour Blend

  • Blanched Almond Flour
    • The base in the flour blend.  Almond flour produces a light and fluffy cake-like bake.  Which makes it a great option for cakes, cupcakes, muffins, and even gluten free cookies.  I will always recommend a blanched, super-fine almond flour.  This means the flour is ground as fine as it can be (before turning into butter), and the skins are removed.
  • Arrowroot Starch/Flour
    • Flour and starch are used interchangeably in the package titles.  Arrowroot aids in the tender texture we like in baked goods.  It also adds structure to the crumb.  
  • Coconut Flour
    • Ground from dried coconut meat, coconut flour is super absorbent.  It should be blended with other flours as it does not work well as a 1:1 swap.  Its absorbency allows swapping granulated sugar for liquid sweeteners –  like maple syrup or honey.  I also find it counter-balances other wet ingredients in the recipe.
  • Tapioca Starch/Flour
    • Another where flour and starch are used interchangeably in package titles.  Tapioca adds a little more chew to the baked good – where normally we’d get that from gluten in all-purpose flour.  And I have found in baked goods, it gives a ‘crisp’ exterior.

Tips For Making Gluten Free Chocolate Chip Muffins

  • Use blanched, super fine almond flour – As the name implies, the almond flour should be super fine to avoid unwanted texture or ‘bite’.  Additionally, blanched almond flour means the almond skins have been removed.
  • Coconut sugar makes bakes, bake darker – It is just a natural occurrence because coconut sugar is darker.
  • Don’t worry about a few lumps in the batter –  Muffin batters are typically lumpy and mixed just until all of the ingredients are incorporated.  A few lumps are ok and they bake themselves out.
  • Toss the chocolate chips with a little arrowroot powder – This helps the chocolate chips from settling at the bottom of the muffin. 
  • Try not to make substitutions – I say this only because I have only tested the recipe as written.  Anything else, and I can’t say or guarantee that the muffins will turn out!
  • Use a cookie scoop to portion the batter into the muffin liners – A cookie scoop is a super helpful tool because it makes portioning the batter easier, and with less mess!
  • Only bake at the high temperature (425F degrees) for 5 minutes – We bake at the high heat for a few minutes to allow the leaveners in the muffins to rapidly work and give the muffins a puff.  Any longer and we are likely to loose that benefit, and then you’ll be left will improperly baked muffins.
Gluten free chocolate chip muffins stacked on a wire rack


Will a 1:1 gluten free flour work instead?

Probably not. In my experience, the 1:1 gluten free flours are much drier than the almond flour blend and the ratio of other ingredients would likely need to be adjusted.

Why are the muffins so dark?

Great question! The coconut sugar is what makes these muffins darker than your traditional traditional Chocolate Chip Muffin.

With all of the coconut ingredients, do these muffins taste like coconut?

No, the muffins don’t taste like coconut. There is no discernable coconut flavor in the flour blend, sugar, yogurt, or oil.

What do the muffins taste like then?

The muffins taste like a bakery style muffin. They are tender, yet slightly dense like a muffin should be. Chocolate chip is the primary flavor and the coconut sugar offers a balanced sweetness.

Can I swap (some/all) of the coconut ingredients for different ingredients?

It’s hard to say, as I have not tested these muffins any other way than the recipe is written. Flour, sugar, yogurt/fat, and oil/butter all behave differently – regardless of the ratio. It is possible you may have success replacing the coconut sugar with granulated or cane sugar.

Why do you bake the muffins at a higher temperature to start, then reduce the heat?

The quick high heat activates the leaveners in the muffins, which contributes to their puff. Reducing the heat then allows the muffins to bake thoroughly and evenly.

How should I store the muffins?

If you have any leftovers (!), the muffins will last for about 3 days covered at room temperature. Beyond that, and they will likely start to get stale.

Breakfast muffins arranged on a wire rack
Two chocolate chip gluten free muffins stacked on top of each other on a small white plate
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5 from 2 reviews

Gluten Free Chocolate Chip Muffins

Yield: 4 Muffins
These Gluten Free Chocolate Chip Muffins are your answer to a small batch, gluten free, and naturally sweetened bakery style muffin!  This is an easy small batch recipe for 4 tender muffins made with an almond flour blend, perfectly sweetened with coconut sugar, and studded with plenty of chocolate chips.
Prep10 minutes
Cook13 minutes
Total23 minutes



  • Preheat oven to 425F degrees and adjust the oven rack to the middle position. Line a muffin/cupcake pan with 4 cupcake liners.
  • In a small mixing bowl, sift together the almond flour, arrowroot flour, coconut flour, tapioca flour, coconut sugar, baking powder and soda, and salt.
  • To keep the chocolate chips from sinking – In a small bowl, add the chocolate chips and a couple sprinkles of arrowroot flour to coat the chocolate chips.
  • In a medium mixing bowl, add the egg, yogurt, oil, and vinegar. Stir until well combined and creamy. Sprinkle the dry ingredients over the wet ingredients and stir the batter until no dry streaks remain. It is ok if there are a few lumps. Add the chocolate chips and stir just until mixed. Scoop the batter equally into the prepared muffin liners. Sprinkle the tops of the muffins with Turbinado sugar (if using). You can also add a few extra chocolate chips to the tops of the muffins.
  • 425F degrees for 5 minutesThen reduce the heat to 350F degrees and continue to bake for another 7 to 8 minutes, or until the tops of the cupcakes are golden brown and a toothpick inserted in the middle comes out mostly clean. Cool in the pan set on a wire rack for 10 minutes, then transfer the muffins to the wire rack to cool completely. Enjoy!
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  • Bake Temperature – Baking at a high temperature (425F degrees) for the first 5 minutes, then lowering the temperature will make the muffin tops puff up. 
  • 1:1 Gluten Free Flour – I have not tested this recipe with a 1:1 Gluten Free Flour blend.  I would recommend following the recipe for Chocolate Chip Muffins.  Swap the flour 1:1 and the chocolate chips for 1/4 cup of chocolate chips.
  • Non-Gluten Free Alternative – I would recommend following the recipe for Chocolate Chip Muffins.  
Course: Breakfast
Cuisine: American
Author: Erin Cernich
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you!

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