Gluten-Free Chocolate Cupcakes

Gluten-Free Chocolate Cupcakes – Rich, moist chocolate cupcakes, topped with whipped chocolate ganache.

Gluten-Free Chocolate Cupcakes

The wait is finally over! I’ve found you a gluten-free cake that I don’t just think you’ll like, I think you’ll love! Many of you have asked for a gluten-free cake for a while, but I needed to do some research and testing before I recommended anything because if I’m going to suggest a flourless alternative to my favorite chocolate cake, one that’s rich, flavorful, and moist, I’m going to make sure you can hardly tell a difference.
As I researched different gluten-free cake recipes, I kept getting turned off by the use of coconut flour in so many of them. I’ve used coconut flour in my baking in the past and just haven’t loved it. It has a certain taste and texture you can notice and that’s definitely something I wanted to stay away from.
I finally came across this Decadent Chocolate Cake recipe by Mel’s Kitchen Cafe (which she originally found on the Good Dinner Mom website), and was immediately intrigued by the fact that it uses cooked Quinoa and doesn’t have an ounce of a flour-like substitute in it! I was also drawn in by Mel’s mouth-watering description of the cake, “This is definitely one of the most decadent, rich, moist cakes I’ve ever tasted.” Since I’ve made several of Mel’s recipes before, I knew I could trust this statement, and so, I got to work.
I decided to start by making the recipe exactly as Mel wrote it, and like her, I didn’t say a word to my family about what was in the cupcake. In fact, I went through three rounds of taste testing with my family, extended family, and friends to ensure that this recipe would pass as unrecognizable gluten-free cupcakes.

Round 1

So, in round one, both my husband and son, two of this world’s toughest cake critics, loved the cupcakes. My son had no idea they were any different from my normal chocolate cake recipe, and my husband, whose favorite cake ever is my chocolate cake, did notice a slightly different but had no problem finishing his cupcake and afterward gave me the thumbs up.

Round 2

In my second round, I decided to use coconut sugar instead of granulated sugar. You’ll see in the recipe below that I ground up the coconut sugar into a fine powder-like consistency. If you use coconut sugar in your baking, you know that it has a grainy texture more like brown sugar than the finer texture you get from white sugar. I was afraid of getting a heavy, dense cake because of the thicker sugar granules, so I had the idea to grab my Magic Bullet and grind them up. I think this helped to keep the cupcakes light and fluffy, while still sweet and rich. Again, these cupcakes passed the taste test with Ryan and Westin, as well as some friends.

Round 3

In my final round, I added an extra egg and two scoops of my favorite chocolate protein powder by Ideal Fit (it’s the only one I’ve tried that doesn’t have a weird aftertaste, and I love that it uses minimal but quality ingredients – I have it every day, either in a shake or just as a post-workout drink), to see if I could make an even healthier cupcake while still maintaining the rich, decadent chocolate taste. My taste testers in this round included Ryan and Westin, along with my mom, my brother, my sister-in-law, and a couple of close friends – all of which were blown away by the fact that these cupcakes were made with Quinoa and protein powder. Again, I didn’t tell them beforehand that there was anything different about these cupcakes, and again, they all gave me thumbs-up, lick-the-plate-clean reviews.
So, now it’s your turn! Check out this gluten-free chocolate cupcakes recipe, give it a try and let me know what you think. If you’re aiming for gluten-free, just leave out the protein powder. You could also substitute the milk with coconut milk, the butter with melted coconut oil, and the heavy cream with coconut cream for a vegan version.
Also, if you liked what you found here, follow me on Instagram @cakebycourtney for the best tips and recipes on all things cake!

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Gluten Free Chocolate Cupcakes

Yield 21 cupcakes or 2-layer 8-inch round cake

Rich, moist chocolate cupcakes with whipped chocolate ganache.


For the Chocolate Cupcakes/Cake

  • 2 cups (370 g) Quinoa, cooked and cooled (about 1/2 cup uncooked - and cook the Quinoa in water, not broth)
  • 5 large eggs, room temperature
  • 1/3 cup (80 g) milk 
  • 2 teaspoons (8.4 g) pure vanilla extract
  • 3/4 cup (169.5 g) unsalted butter, melted and cooled
  • 1 cup, plus 3 tablespoons (124.4 g) unsweetened cocoa powder (I use dark cocoa powder)
  • 1 1/2 cups (300 g) coconut sugar (or granulated)
  • 1 1/2 teaspoon ( 6 g) baking powder
  • 1/2 teaspoon (2.8 g) salt
  • 1/2 teaspoon (2 g) baking soda

For Whipped Chocolate Ganache

  • 2 cups (300 g) dark chocolate chips
  • 2 1/2 cups (577.5 g) heavy whipping cream


For the Chocolate Cupcakes or Cake

  1. Preheat your oven to 350 degrees F. Line your cupcake pans with cupcake liners. Fill any empty cupcake spots with a little water. For the cake option, spray two 8-inch round cake pans with non-stick cooking spray and line the bottoms with parchment paper. Spray again. Set aside.
  2. Using a blender or food processor (I used a Magic Bullet), grind your coconut sugar into a fine powder. Set aside. If using granulated sugar, DO NOT grind it.
  3. In a blender or food processor, combine the cooked Quinoa, eggs, milk, vanilla and butter. Blend until the mixture is smooth and silky.
  4. In a stand mixer fitted with the paddle attachment, combine the finely ground coconut sugar, cocoa powder, baking powder, baking soda, and salt. Mix the ingredients for about 30 seconds.
  5. With the mixer on low speed, add the Quinoa mixture to the dry ingredients and stir until combined. Turn the mixer off, scrape down the sides of the bowl and mix again for another 30 seconds on low speed.
  6. Fill your cupcake liners about 2/3 full with the batter. I like using a large cookie scoop to distribute the batter evenly. For the cake option, pour half of the batter into one pan and smooth out the batter with an offset spatula or spoon. Pour the rest of the batter into the second pan and evenly spread the batter.
  7. Bake cupcakes for 12-14 minutes. Bake the cake layers for 20-25 minutes (check at 20 minutes with a toothpick).
  8. Let cool on wire rack for 10 minutes before removing from the pans. 

For the Whipped Chocolate Ganache

  1. Heat the whipping cream in a saucepan over medium heat until it reaches a gentle simmer. Mean while, pour the chocolate chips into a medium bowl.
  2. Once the cream reaches a simmer, pour it over the chocolate chips and let sit for about 5 minutes.
  3. Whisk the cream and chocolate chips until glossy and smooth. Cover the bowl with plastic wrap and refrigerate until completely chilled, about 2-3 hours. (I sped this up and put the bowl in my freezer for about 30 minutes.)
  4. When the chocolate ganache is chilled, use an electric mixer (handheld or stand) to whip the mixture into soft peaks.          

Courtney Rich

I’m a self-taught baker, obsessed with cake.

I long ago ditched box mixes in pursuit of melt-in-your-mouth, to-die-for flavor combinations, fillings and textures. I believe cake must be decadent, life-changing and worthy of celebration! And I believe anyone should be able to bake that kind of cake – and I’m here to teach you just that!

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Leave a Comment


    1. I actually have a vegan chocolate cake that you can make GF with GF flour. I haven’t tried these cupcakes in vegan form.

  1. Loved it! I made it as a cake for my family and everyone loved it. It’s more dense than a traditional cake but my husband preferred it. I didn’t add the protein powder.

  2. Do you know if it matters whether I use white or red quinoa? Thanks for sharing this recipe! Super excited to make for my birthday!

  3. Could the chocolate ganache be used as a filling for a 3 layer cake or would it be too soft? I’m looking for a rich dark chocolate filling

  4. Hi! I’m planning on making your quinoa chocolate cake. My sister in law is also dairy intolerant. Am I good to subtitle for coconut milk and dairy free butter? And do you have brand recommendations? Thanks!

  5. Just made these and they are delicious. Mine did fall in the centre and I’m wondering if there’s something I can do to prevent this?

  6. I LOVE this recipe! I’ve tried it regular snd dairy free and it always turns out amazing! Courtney thank you for creating recipes that everyone can enjoy!