The Best Gluten-Free Chocolate Cupcakes

May 14, 2024

If I didn’t tell you, you’d have no idea these Chocolate Cupcakes were gluten-free AND packed with protein because they are just as rich and delicious as my popular go-to chocolate cake. How can that be? I’m share all the details and this easy-to-make recipe below!

Chocolate cupcakes with vanilla buttercream.

Gluten-Free Chocolate Cupcakes

Truly, you’ll take one bite of these cupcakes and be shocked at the moisture, texture, and flavor! Gluten-free has never tasted so good. Plus, we’ve added some protein without compromising flavor!  



Yup, I said it, quinoa!  

A chocolate cupcake on a pink background.

Years ago, I 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! 

Much like my cakes with cooked oatmeal, this cake gets so much moisture from the quinoa.

We’re also using my favorite, dark chocolate cocoa powder for the best chocolate flavor. This cocoa powder is also high in fat, which helps create and retain the moisture in our baked goods too.

A cupcake split in half.

Two Frosting Options

Vanilla Buttercream

For these cupcakes, I made a batch of my go-to, easy-to-make Vanilla Buttercream. For a simple slather of buttercream, a half batch will be plenty. If you want to swirl a bit more on top of the cupcakes, I’d plan on making the full batch.

Chocolate Ganache

Another option would be a simple chocolate ganache, using 2 cups dark chocolate chips and 2.5 cups heavy whipping cream. To make the ganache, follow these steps:

  • 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.
  • Once the cream reaches a simmer, pour it over the chocolate chips and let sit for about 5 minutes.
  • 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.)
  • When the chocolate ganache is chilled, use an electric mixer (handheld or stand) to whip the mixture into soft peaks

Cupcake Liners

Instead of traditional cupcake liners, I love using these baking cups from My Mind’s Eye. You’ll just put them on a baking sheet, making sure there’s about an inch or two between each baking cup, and bake the for the same amount of time as you would in the recipe with a cupcake pan.

MOre Chocolate Cakes to love

Chocolate cupcakes with vanilla buttercream.

Gluten-Free Chocolate Cupcakes

5 from 5 votes
Protein packed, gluten-free chocolate cupcakes made with quinoa.
Servings 21 cupcakes or 2-layer 8-inch round cake


  • 2 cups (370 g) Quinoa, cooked and cooled (about ½ cup uncooked – and cook the Quinoa in water, not broth)
  • 5 large eggs, room temperature
  • 1/3 cup (80 g) buttermilk, room temperature
  • 1 teaspoon (4.2 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) granulated sugar
  • 1 1/2 teaspoon (6 g) baking powder
  • 1/2 teaspoon (3 g) salt
  • 1/2 teaspoon (2 g) baking soda


  • 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.
  • In a blender or food processor, combine the cooked Quinoa, eggs, buttermilk, vanilla and butter. Blend until the mixture is smooth and silky.
  • In a stand mixer fitted with the paddle attachment, combine the sugar, cocoa powder, baking powder, baking soda, and salt. Mix the ingredients for about 30 seconds.
  • 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.
  • 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.
  • Bake cupcakes for 12-14 minutes. Bake the cake layers for 20-25 minutes (check at 20 minutes with a toothpick).
  • Let cool completely before adding frosting.
Course: Dessert
Cuisine: Cupcake
Keyword: chocolate, gluten free, gluten free cupcakes

Join the Conversation

  1. 5 stars
    Love the thinking outside the box cooking that you have. Thanks for sharing with us.

  2. Steve Kearns says:

    I’m making these as I type. My niece can’t have gluten so when I saw this I had to try them.

  3. Steve Kearns says:

    I made today and everyone loved them.

Leave a Reply

Your email address will not be published. Required fields are marked *

Recipe Rating

Copyright © 2022 LEMON & LIMES.
Made with by Loft.Ocean. All rights reserved.
Popular Search: