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Gluten Free Chocolate Cupcakes


These gluten free chocolate cupcakes are super moist, and amazingly chocolatey! They have the nutrition of a muffin, but taste like cake!

gluten free mini chocolate cupcake with chocolate frosting on cooling rackgluten free mini chocolate cupcake with chocolate frosting on cooling rack

How Do You Make Gluten Free Chocolate Cupcakes From Scratch?

Making gluten free cupcakes uses basically the same method as regular chocolate cupcakes. This recipe calls for flax + water instead of an egg which is the main difference between this recipe and other recipes.

The nice thing about using gluten free flours is that you don’t have to worry about overmixing, because you are never going to create too much gluten! But for all intensive purposes, you still mix the dry and wet ingredients separately and then add them together at the end.

gluten free mini chocolate cupcakes with chocolate frosting on cooling rack

Which Gluten Free Flour Is Best for Cake?

According to the gluten free experts, the flour that has been found to work best in the most variety of baked goods is the King Arthur Flour gluten-free blend. It contains both white and brown rice flour and two types of starches – potato and tapioca. Those four ingredients have been found to be the key to a gluten free blend that works almost as good as a wheat flour.

Do Gluten Free Cupcakes Taste Good?

If you have done any amount of baking with gluten free flours, you can probably attest to the fact that many of them taste awful: Sorghum flour, amaranth flour, soy flour – yuk! However, some of the gluten free flours actually create baked goods that taste just as good if not better than those made with wheat flour.

Believe it or not, rice and nut flours hold moisture better than wheat flour and are able to create a better tasting product that lasts longer. So basically, just because a flour is “gluten-free” does not necessarily mean it tastes terrible.

gluten free mini chocolate cupcake with chocolate frosting on cooling rack
gluten free mini chocolate cupcake with chocolate frosting on cooling rack
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3.7 from 29 votes

Gluten Free Chocolate Cupcakes

These gluten free chocolate cupcakes are super moist, and amazingly chocolatey! They have the nutrition of a muffin, but taste like cake!
Cook Time25 minutes
Total Time25 minutes
Course: Dessert
Cuisine: American
Servings: 12
Calories: 312kcal


  • 12 standard cupcake liners
  • 2 3/4 cup King Arthur Gluten Free Flour Blend
  • 1/2 teaspoon salt
  • 3/4 cup cocoa powder, unsweetened
  • 1 3/4 cup sugar
  • 1 1/2 teaspoon baking powder
  • 2 teaspoon baking soda
  • 2 tablespoon flaxseed, ground
  • 1/4 cup water
  • 2 teaspoon vanilla extract
  • 1/2 cup coconut oil
  • 1 cup soy milk
  • 1 cup water


  • Preheat oven to 350 degrees. Place cupcake liners into a muffin pan.
  • Mix ground flax with 1/4 cup of water and allow to sit while gathering and mixing other ingredients.
  • Sift flour, salt, cocoa, sugar, baking powder and baking soda in a large bowl.
  • In a separate smaller bowl, mix together flax eggs (the water and flax that has been sitting), vanilla, oil, milk (we used almond milk) and boiling water.
  • Mix wet ingredients into dry ingredients. Pour an even amount into each cupcake liner.
  • Bake on middle rack for 20-25 minutes and check for doneness by inserting a toothpick into a cupcake, looking for minimal residue, which will indicate that they are finished baking. The tops should be firm when they are done, too.
  • Allow to cool before icing.


Calories: 312kcal | Carbohydrates: 54g | Protein: 5g | Fat: 11g | Saturated Fat: 8g | Sodium: 323mg | Fiber: 5g | Sugar: 31g
Keyword : Vegan Gluten Free Cupcake


Natalie Monson

I'm a registered dietitian, mom of 4, avid lover of food and strong promoter of healthy habits. Here you will find lots of delicious recipes full of fruits and veggies, tips for getting your kids to eat better and become intuitive eaters and lots of resources for feeding your family.

Learn More about Natalie

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Recipe Rating


Sounds awesome and delicious. Could you please recommend options / settings for convection microwave baking for this receipe? Thank You!

Hi Ruchi,

Although I don’t own a convection microwave, it is my understanding (through a search online) that you would use the same settings. Does your convection microwave have a setting for the temperature I used here? If so, I would use that. But, even before doing this, check your user manual or online on the manufacturers website. That should be your first route as should be the important fact that you would need the proper baking tools to use inside your convection microwave.

hi i love to get your winning rcipee from earhfare.you got the picture but not the rcipee.also could you find me the healthy rcipee winners from earthfare as i think they have deleted them by accident.i been trying for days and hours.could you also tell me if you ever come across apple cake or slice low fat that actually you can taste the alpple and cinnomomn as i love that combo.i once tasted a biscuit stuffed with apple chunks it was delicious love a rcipee for that.please could you email me the winnimg rcipees from eatrthfare as well as yours i love healthy and winning.oh yes my email ismany thanks if you can as you are one of the winners and they promised to publish.

Made these with my kids. They were delicious and really light. I used a cup of dark brown sugar and found they were fine without being too sweet like normal cupcakes. I didn’t even bother with icing!

I would love to try some of the stuff you post but it is really difficult since you use cups as a measurement. If you post our recipes in grams as well more people would benefit from this.

5 stars
Yummy! Made 24 regular cupcakes for me though. Also not sure what frosting they are referring to in the directions. : /

5 stars
I have many allergies, I try to feed my little gluten free and dairy free, and my bestie is vegan. We made these together and all loved them!!

5 stars
These were my first vegan cupcakes. Loved them! I used a vegan icing I had bought from Whole Foods. –you can’t fail on goodness there. 🙂

I noticed that xantham gum was not used. Was it present in the gf flour that you used or did you skip it?

1 star
Followed the recipe, but unfortunately cup cakes came out almost unedible, very dry, crumbly and not nice at all.