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Chocolate Gluten Free Cupcakes

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This is small batch recipe for Chocolate Gluten Free Cupcakes are made with an almond flour blend, are naturally sweetened with coconut sugar, and are dairy free.  The cupcakes are incredibly moist, rich in chocolate flavor, and a great base recipe for any occasion!  

Close up of a frosted gluten free chocolate cupcake

Chocolate Gluten Free Cupcakes

Is there anything better than a soft, fluffy, and moist chocolate cupcake?  Well, I’m sure that there is, but for the sake of this recipe post, I’ll just say these are the best gluten free chocolate cupcakes I’ve ever had!  Much like their gluten counterpart – chocolate black forest cupcakes – these cupcakes are great for any occasion and any day of the week.

One of the things that makes chocolate cupcakes so wonderful is that they are a great classic recipe that can take on just about any flavor of frosting.  This recipe, for example, features a strawberry butter free frosting.  Chocolate and strawberry are one of the dynamic duos of flavor and the same ones I use in the small gluten free chocolate cake recipe!  

For these gluten free cupcakes, there are just a few more delicious features worth highlighting:

  • Rich chocolate flavor – If the title says chocolate, I want to taste chocolate!  And you won’t be disappointed with the chocolate flavor in this recipe.
  • Light and fluffy – A good cupcake (and cake) should be light and springy (in my opinion).  That is these cupcakes.
  • Super moist – I have yet to find a better word for moist, but let’s face it, do we need to?  It describes perfectly what to expect when you bite into one of the cupcakes.  No dry cardboard cakes here!
  • You’ll never know they are gluten free – I’ve tested these with some pretty finicky tastebuds and none were able to discern that the cupcakes were gluten free.  Thanks in part to the almond flour blend which yields a soft and light cake crumb.

Gluten Free, Dairy Free, Refined Sugar Free Cupcakes

  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 – Unless you swap the coconut milk with a dairy counterpart, these cupcakes are dairy free!
  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.  

With so many ‘frees’ in the recipe, you may be wondering what do these cupcakes taste like?  Well, as I’ve outlined above, they taste just as you would expect and want a good chocolate cupcake to taste like.  A soft cake texture with rich chocolate flavor.

Small batch gluten free chocolate cupcakes on a cake platter

What You Need To Make Gluten Free Chocolate Cupcakes


I have provided a little more detail in the box below the ingredients list on the flours included in my almond flour blend

  • Almond Flour 
  • Arrowroot Flour 
  • Coconut Flour 
  • Tapioca Flour 
  • Dutch Processed Cocoa Powder – I like to use Dutch processed cocoa because it isn’t as bitter as natural cocoa.  Additionally, it produces a rich chocolate flavor.
  • Coconut Sugar – You can find coconut sugar at most grocery and natural food stores these days.  I like to use Anthony’s (linked in the recipe), or Big Tree.
  • Baking Powder and Baking Soda – We use both to give the cupcakes the proper cupcake lift.
  • Salt – Balances out and enhances all of the flavors.
  • Egg – 1 large egg is all we need.
  • Coconut Oil – The coconut oil is solid, which is also termed cold-pressed.
  • Coconut Milk – I use unsweetened So Delicious coconut milk.  It is super creamy and not watered down like other brands can be.
  • Apple Cider Vinegar – The apple cider vinegar works with the baking soda for that cupcake lift.
  • Vanilla Extract – Flavor!
  • Hot Coffee – I recommend a good medium brew, or you can also use hot water.  Coffee enhances cocoa flavor.

Baking Equipment

  • Muffin/Cupcake Pan
  • 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.
Row of frosted chocolate gluten free cupcakes

Tips For Making Chocolate Gluten Free Cupcakes

  • Use blanched almond flour – As I outlined above, blanched almond flour is ground finer.  On the other hand, almond meal may yield more of texture in the cupcakes.
  • Dutch process cocoa for a rich chocolate flavor – I rarely use natural cocoa powder because I find it too acidic.  I prefer Dutch processed cocoa because it has a bold chocolate flavor and isn’t as bitter.
  • Use cold pressed coconut oil – Yes, I know it seems counterintuitive to start with solid coconut oil and melt it, as opposed to just using liquid coconut oil.  However, solid coconut oil (cold-pressed) has more fat in it, which is ideal for baking, whereas liquid coconut oil has had most of the fat removed.
  • Try the recipe with the coffee – Coffee and cocoa in baked goods go together like peanut butter and jelly.  Coffee amplifies the cocoa flavor, and no, it does not make the cupcakes taste like coffee!
  • Don’t fret the thin batter – I find a lot of cake batters – especially chocolate – are thin.  And I always freak out, but then I am surprised to see how the cake baked into a super light and fluffy treat!
  • Watch the bake time – In my experience, gluten free bakes take a tad longer to bake.  Just keep an eye on the cupcakes and start checking at the minimum time noted.  When testing for doneness, the cupcakes will be springy to the touch and a toothpick inserted in the middle will have a few crumbs.
  • Store the cupcakes at room temperature – Unfrosted cupcakes store great in a covered container at room temperature.  They will stay moist for about 2 days.  Beyond that, they will likely start to dry out.
Single glute free chocolate cupcake on a mini cupcake stand

Common Questions For Making Gluten Free Chocolate Cupcakes

Can this cupcake recipe be doubled?

I have not tested a larger batch and I can’t say for certain. You can certainly try it and let me know how they turn out!

Will a gluten free 1:1 flour work instead of the almond flour blend?

In my experience, a swapping a gluten free 1:1 blend doesn’t work for my gluten free recipes. The almond flour blend and 1:1 gf flour seem to require different ratios of wet and dry ingredients to turn out correctly.

All I have is natural cocoa powder. Will that work instead of the Dutch processed cocoa powder?

I think natural cocoa powder will work fine. Just note that your cupcakes will likely bake into a lighter color, and the chocolate flavor may not be as bold.

Can I substitute a different sugar or sweetener?

Granulated sugar will work as a 1:1 swap for the coconut sugar. Otherwise, I don’t have experience with sugar-free sweeteners (i.e. monk fruit or stevia), and liquid sweeteners will throw off the ratios.

Is the coffee necessary, or can I just use hot water?

Hot water will work just fine.

The batter seems really thin and runny. Is that normal?

Yes! The batter should be thin, and it will bake up into light and fluffy cupcakes.

What is the deal with only 5 cupcakes? Why not 4, or even 6?

I have tested and tested, and 5 cupcakes is the right amount with the ratio of ingredients in this small batch recipe. Any more or any less may require trying to ‘halve’ an egg.

Do you have any other frosting recipes besides the Strawberry frosting linked in the recipe?

I do! Check out the frosting category – you’ll find vanilla, chocolate, marshmallow, and even whipped coconut cream if you want something lighter.

Gluten free chocolate cupcakes arranged om a white table

More Small Batch Cupcake Recipes

Gluten free frosted chocolate cupcake on a mini cake stand

Chocolate Gluten Free Cupcakes

Yield: 5 Cupcakes
This is a small batch recipe for Chocolate Gluten Free Cupcakes are made with an almond flour blend, are naturally sweetened with coconut sugar, and are dairy free.  The cupcakes are incredibly moist, rich in chocolate flavor, and a great base recipe for any occasion!  
Prep10 minutes
Cook15 minutes
Total25 minutes


  • 1 – Muffin/Cupcake Pan



Gluten Free Chocolate Cupcakes

  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Line a muffin/cupcake pan with 5 cupcake liners.
  • In a small mixing bowl, whisk together the almond flour, arrowroot flour, coconut flour, tapioca flour, cocoa powder, coconut sugar, baking powder and soda, and salt.
  • In a medium mixing bowl, add the egg, melted coconut oil, coconut milk, vinegar, and vanilla extract. Whisk until completely combined.
  • Sprinkle the dry ingredients over the top of the wet ingredients. Stir until no dry streaks remain. Add the hot coffee (or water), and stir until combined.
  • Bake the cupcakes for 14 to 15 minutes, or until a toothpick inserted in the middle comes out mostly clean. Cool the cupcakes in the pan set on a wire cooling rack for 5 minutes, then transfer the cupcakes to the rack to cool completely.
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Course: Dessert
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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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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