Chocolate Quinoa Cupcakes

 This is one of my favorite chocolate cupcake recipes and they happen to be gluten free, but they’re so rich, chocolatey and delicious that you certainly won’t miss the flour. 

Chocolate Quinoa Cupcakes

These cupcakes. My first experience with quinoa cake was in the bakery I used to work at. My boss liked making gluten free desserts and one day he presented me with this. It was like heaven. Seriously one of the richest, most amazing desserts I’ve ever eaten. Like slap you in the face, hello chocolate, is this real life? chocolatey goodness.

Chocolate Quinoa Cupcakes

And it’s gluten free! How can you make a gluten free cake, you ask? Here comes the science! *said in a sing song voice*

Typically, cakes are made with wheat flour. Wheat flour is unique because when a liquid and flour mix and you knead it or mix it, it forms gluten networks. Gluten networks are what create the lovely structure in bread, but in cake, you want to minimize gluten formation, while still using minimal gluten to make a nice cake structure. How? Sugar and butter, that’s how! Sugar acts as a scissors and cuts through the gluten networks. The fat coats the flour and prevents it from forming networks. That’s why bread is low in sugar: you wouldn’t have the delicious air pockets in bread if the sugar was cutting up the networks.

Chocolate Quinoa Cupcakes

So how in the world do you make a delicious and fluffy cake without flour?

In this particular recipe, the flour is replaced by cooked quinoa and a large quantity of unsweetened cocoa powder. When I edit cookie or cake recipes to make them chocolate, you have to get rid of some of the flour for the cocoa powder because cocoa powder has the consistency of flour with fewer calories but no gluten. That’s why a lot of gluten free recipes have ample amounts of cocoa powder: it can provide a little bit of structure and it’s gluten free. When you make this cake, the quinoa and cocoa powder together act as a flour replacement; however, because neither contain gluten, the cupcakes don’t have the fluffy structure of a cupcake. Rather, these cupcakes are dense and chocolatey, but still with a cake-like texture.

Chocolate Quinoa Cupcakes

And finally, one of the major components of this recipe that adds structure are the eggs. This recipe doesn’t make a very big batch, so relatively speaking, four eggs is a lot of eggs for this recipe. In any cake recipe, eggs provide structure. In addition, they also help with leavening.

When you make these, you will be able to see the tiny quinoa grains in the cupcake. I thought this would be off-putting, but it adds to the texture and chewiness of the cupcake.

Chocolate Quinoa Cupcakes

Tips for these cupcakes:

  • Use good cocoa powder! It’s a major part of this recipe. I recommend Hershey’s Special Dark.
  • Fill the cupcake liners 3/4 full. The cupcakes don’t rise a ton because they are gluten free, so you want a nice big cupcake!

But don’t be fooled by the gluten free tag! These cupcakes are not low calorie. They have plenty of butter and oil to keep things moist and delicious. But honestly, if you don’t run to your kitchen now and make these, I will be very disappointed in you.

Chocolate Quinoa Cupcakes

Chocolate Quinoa Cupcakes
Recipe Type: Gluten Free Cake
Author: Adapted by Brita
Prep time: 35 mins
Cook time: 13 mins
Total time: 48 mins
Serves: 12
This gluten free cake is so rich, delicious and fantastic that nobody will even know it’s gluten free. The secret ingredient is quinoa instead of flour, which is high in protein and makes a fantastic cake ingredient.
  • Quinoa Cupcakes:
  • 2 cups cooked quinoa*
  • 4 eggs, room temperature
  • 1/3 cup almond milk (or cow’s milk, soy milk, coconut milk etc.)
  • 1 teaspoon vanilla extract
  • 1/2 cup (1 stick) melted butter
  • 1/4 cup canola oil
  • 1 cup sugar
  • 1 cup unsweetened cocoa powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 and 1/2 teaspoons baking powder
  • Cream cheese frosting:
  • 4 ounces cream cheese, softened
  • 4 ounces (1 stick) butter, softened
  • 2 cups powdered sugar
  • 1/4 cup cocoa powder (I used Hershey’s Special Dark)
  1. Quinoa Cupcakes:
  2. *Two cups cooked quinoa is a little more than 3/4 cups dry quinoa.
  3. Preheat the oven to 350 degrees and then place cupcake liners in cupcake pan.
  4. Boil the uncooked quinoa with 1 and 1/2 cups water for 10-15 minutes. You will be able to see the tiny white dot on the inside and the “shell” will be clear. I recommend cooking it to a maximum of 15 minutes so it’s extra soft for the cake. Then let cool. This takes about fifteen minutes.
  5. In a blender or food processor, combine the eggs, almond milk (or preferred milk) and vanilla extract then blend for ten seconds to combine.
  6. Add the cooked and cooled quinoa along with the melted and cooled butter and canola oil hen blend until completely smooth, about thirty seconds to one minute.
  7. Sift together the dry ingredients in a large bowl (cocoa powder, sugar, baking powder, baking soda and salt).
  8. Add the wet ingredients in the blender to the bowl with the dry and mix together until well-combined.
  9. Divide the batter between the cupcakes and bake for about 12-15 minutes or until a toothpick comes out clean.
  10. Cream cheese frosting:
  11. Cream together the butter and cream cheese. Add the powdered sugar and the cocoa powder. Add more powdered sugar or milk depending on what consistency you would like.




  1. Your recipe says to mix the dry ingredients, including sea salt. I didn’t see sea salt in the ingredients list. How much should I use? Thank you!

  2. I used coconut oil instead of butter too. I think I would halve the cocoa too, it’s really strong chocolate taste, but thank you, it’s a delicious and moist recipe. 🙂

    • Hi Rosie! Sounds great about the coconut oil! If you want to downplay the chocolate taste, compensate the cocoa for a bit of GF or all-purpose flour (depending on your dietary needs.) The cocoa stands in for flour in this GF recipe and without it, I don’t know how they would turn out! Thanks for your feedback!

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