Flourless Chocolate Cupcakes—made with quinoa!

Flourless Chocolate Cupcakes—made with quinoa!

These special flourless chocolate cupcakes are naturally gluten free and dairy free, and rich and incredibly moist. They’re made with soaked quinoa instead of any sort of flour, but you’d never know it!

These special flourless chocolate cupcakes are naturally gluten free and dairy free, and rich and incredibly moist. They're made with soaked quinoa instead of any sort of flour, but you'd never know it!

You don’t even cook the quinoa

These cupcakes are so incredibly tender and rich, but not at all too sweet. Seriously. Personally, I don’t care for the taste of quinoa. To me, it always seems bitter. I’ve baked with quinoa flour, too, and the results have usually gone right in the circular file 🗑.

Here on the blog, we’ve made gluten free chocolate cake with cooked quinoa before (with remarkable success), but we’ve cooked the quinoa. I know it’s meant to be made with “leftover” quinoa, but I rarely make the stuff so I don’t ever have that on hand.

When you want to bake flourless, you do need something to form the base of the baked good. In the past, we’ve used nut butters like in these Flourless Chocolate Peanut Butter Muffins. To make a Flourless Vanilla Muffin, we used cashews as a base since they have a much more neutral flavor than peanut butter.

This time, we’re soaking raw white quinoa in water overnight (for about 12 hours, but up to 24) before blending it with oil, eggs, and vanilla. Once the quinoa is soaked and drained, it can be used in this recipe or the chocolate cake recipe and will keep in a sealed container in the refrigerator for at least 4 days.

These special flourless chocolate cupcakes are naturally gluten free and dairy free, and rich and incredibly moist. They're made with soaked quinoa instead of any sort of flour, but you'd never know it!

Naturally dairy free

I got the idea for baking with soaked quinoa from my friend Alisa Fleming’s new book, coming out in January 2018, called Eat Dairy Free, and her recipe for Gluten Free Quinoa Pizzetta Crust (on page 263). I’m planning to share her recipe from the book for Dairy-Free Chicken Alfredo in January. It’s just so good, whether you need to be dairy-free or not.

The moment I got my advance copy of Alisa’s book, I started cooking. Right now, my oldest child is dairy free due to some mysterious health issues that only disappear when she, well, doesn’t eat dairy.

That doesn’t mean that I don’t cook and bake with dairy, but I also try to have a comparable treat for my daughter. I can’t wait to talk to you more about that book next month, but for now, we’ll begin with these naturally dairy free chocolate cupcakes.

These special flourless chocolate cupcakes are naturally gluten free and dairy free, and rich and incredibly moist. They're made with soaked quinoa instead of any sort of flour, but you'd never know it!

These flourless chocolate cupcakes have absolutely no trace of the taste of quinoa. I have a powerful sense of smell and a pretty well-trained sense of taste (nearly 10 years of blogging and cookbook writing will do that to you!), and I can’t tell at all. Two of my three children also don’t care for quinoa, and they love these cupcakes.

Since I’m always looking for grab-and-go breakfasts and snacks that I consider actually healthy (to me that means low in refined sugar, high in healthy fat, and high in protein), I made these with Swerve granulated sugar substitute.

I gave the ones that were made with refined sugar to my children as a treat, and the ones made with Swerve to them for breakfast—and insisted they were muffins. They were thrilled with both.

These special flourless chocolate cupcakes are naturally gluten free and dairy free, and rich and incredibly moist. They're made with soaked quinoa instead of any sort of flour, but you'd never know it!

It’s actually super strange to me that these cupcakes are truly so tender and rich. And even though there is a ton of cocoa powder in the recipe, which certainly covers the smell and taste of quinoa, that doesn’t seem to explain the complete lack of quinoa-ness. Mysteries abound!

I can tell you this, though. I plan to continue working with soaked quinoa. I dream of making a vanilla cake with it, but there’s just no way you wouldn’t taste the quinoa-ness then. I know that you can toast quinoa flour to rid it of its bitterness, but then it’s all becoming more complicated than I care for. Stay tuned!

Watch this short (< 1 minute) how to video

Push play ▶️ and see for yourself how easy it is to make these flourless chocolate cupcakes:

Ingredients and Substitutions

As always, unless specifically noted otherwise, I haven’t tried these particular substitutions. These are just my best-educated guesses.

Dairy-Free: It’s already dairy-free!

Egg-Free: There are two eggs in this cake, and you can try a “chia egg” (1 tablespoon ground chia seeds + 1 tablespoon lukewarm water, mixed and allowed to gel), but the eggs are very important in this cake.

Quinoa: I haven’t tried this recipe with any other soaked seed or grain, but I suspect that it would work with anything that cooks in water like a porridge, like teff as I did in my flourless quinoa gluten free chocolate cake. Feel free to experiment! Try to steer clear of anything that has a very strong flavor and that doesn’t pair well with chocolate. Teff and chocolate are very compatible.

Sugar-Free: In preparation for the New Year and feeling virtuous, I’ve made this recipe using Swerve granulated sugar substitute in a gram for gram replacement. The recipe definitely still works, but the color of the baked good is a little different (no biggie) and the batter is thicker. I recommend adding 1 tablespoon of lukewarm unsweetened nondairy milk to the batter to make it easier to scoop.

These special flourless chocolate cupcakes are naturally gluten free and dairy free, and rich and incredibly moist. They're made with soaked quinoa instead of any sort of flour, but you'd never know it! #glutenfree #glutenfreerecipes #flourlesscake #chocolatecake

Like this recipe?

Prep time: Cook time: Yield: 12 cupcakes


2 eggs (100 g, weighed out of shell), at room temperature

6 tablespoons (84 g) neutral oil (like sunflower, grapeseed, canola or vegetable oil)

1 1/3 cups (220 g) soaked and drained raw white quinoa*

1 teaspoon pure vanilla extract

2/3 cup (133 g) granulated sugar (or granulated sugar replacement like Swerve)

3/4 cup + 1 tablespoon (65 g) unsweetened cocoa powder (natural or Dutch-processed)

3/4 teaspoon baking powder

1/4 teaspoon baking soda

1/4 teaspoon kosher salt

*This recipe must be planned for, but it takes quite literally 1 minute of active planning. Rather than listing dry, raw quinoa as an ingredient and then instructing you to soak it for 12 hours, I’ve included the soaked and drained quinoa as an ingredient. Simply place about 1 1/2 cups (by volume, if you like) raw quinoa in a bowl or jar, and add enough tap water to cover by about in inch. Cover and allow to soak in the refrigerator overnight, or for up to 24 hours. Then, drain in a fine mesh sieve or nut milk bag, and measure the soaked and drained quinoa by weight for use in the recipe.


  • Preheat your oven to 350°F. Grease or line a standard 12-cup muffin tin and set it aside.

  • In a blender or food processor, place the eggs, oil, soaked and drained quinoa and vanilla, and blend or process until smooth. The mixture should become lighter in color. You will still see flecks of the quinoa, but process until it’s as smooth as possible. In a large bowl, whisk together the sugar, cocoa, baking powder, baking soda, and salt. Add the eggs and oil mixture, and mix until well-combined. The mixture will be thick. If you’ve used Swerve in place of sugar, add 1 tablespoon of nondairy milk to the batter and mix to combine, so the batter is easier to scoop.

  • Divide the batter among the prepared wells of the muffin tin and spread into an even layer in each well using wet fingers. Place in the center of the preheated oven and bake until the cupcakes are set in the center and spring back when pressed very gently in the center (about 19 minutes).

  • Remove the tin from the oven and allow the cupcakes to cool in the pan for about 10 minutes before turning out onto a wire rack to cool completely. The finished and cooled cupcakes can be stored in a sealed container at room temperature for up to 3 days, or wrapped tightly in plastic wrap and frozen for storage of up to 2 months. Allow to thaw at room temperature before serving.


Comments are closed.

  • HT
    December 29, 2017 at 1:29 PM

    Making these was the best decision I made all day! They are so moist and fluffy. I was out of cocoa powder so I improvised with some hot cocoa mix and slipped the sugar. I also dumped some leftover coffee in just for fun. I can’t stop eating them and my 2 year old keeps demanding more.

    • Nicole Hunn
      December 29, 2017 at 4:23 PM

      Wow, those are a lot of substitutions, HT. I’m glad it worked out!

  • Sora
    December 28, 2017 at 10:32 PM

    What can you do with the leftover soaked quinoa

    • Nicole Hunn
      December 29, 2017 at 10:10 AM

      Make more cupcakes, Sora, make the quinoa chocolate cake, or just cook it and eat it!

  • Mare
    December 27, 2017 at 10:58 AM

    I am now in the no dairy club. I ate your Ricotta Pancakes on Christmas (best pancakes ever!) and then your Cannoli Pie (It is amazing!) for dessert that night . Did Lactaid with both. Oh well. Live and learn. I don’t have issues with the whey protein isolate in the bread, though. Hoping it remains that way! I appreciate that you are looking into no dairy recipes and that you suggest substitutions.

    I only cook Quinoa after soaking, rinsing, and toasting a little in the oven. I wonder how it would be if the Quinoa was toasted? Hum, maybe I will try it and let you know.

  • Theresa
    December 27, 2017 at 9:05 AM

    The bitter taste is due to saponins on the seeds. Rinsing does remove most of the bitterness but moist seeds might also alter your batter consistency. https://www.epicurious.com/expert-advice/does-quinoa-need-to-be-rinsed-article

    • Nicole Hunn
      December 27, 2017 at 10:26 AM

      Thanks for the info, Theresa. The seeds here are soaked, so moisture isn’t an issue.

  • Cristina Moidel
    December 24, 2017 at 11:19 AM

    Hey Nicole, I made these yesterday with coconut sugar instead of white sugar and it does work. They are obviously not as sweet, though. I put a little (Simple Mills) vanilla frosting on them and both kids and husband liked them. Next time I may try half white sugar and half coconut sugar and I’ll let you know how it goes. Thanks for the recipe!

  • kate
    December 23, 2017 at 5:52 AM

    I always read “kosher salt”. Is that the regular Morton Kosher Salt (med sized crystals) or Morton Kosher Table Salt (smaller crystals). Seriously, I find this very confusing regarding which size to use when cooking and baking. I sense I can trust your advise. Thank you in advance for all the time and energy you put into your baking/cooking.

    • Nicole Hunn
      December 23, 2017 at 9:44 AM

      Kate, kosher salt is medium sized crystals of salt, not table salt, which is fine.

  • Kathy
    December 22, 2017 at 11:24 PM

    Ooh I really want to try this. Looks really simple and the cake looks moist!

  • Darlene
    December 22, 2017 at 6:57 PM

    These look amazing Nicole! I, like you, don’t like the strong taste of quinoa … I made your chocolate cake, it was pretty good, but I could still taste the hint of quinoa. In this recipe you have mentioned Teff as an alternate, would I substitute gram for gram with the teff?

    • Nicole Hunn
      December 23, 2017 at 9:42 AM

      As I explain in the post, Darlene, you can try substituting teff (yes, it would be gram for gram) but I haven’t done it so I don’t really know for sure! I’m sorry you didn’t like the chocolate cake with quinoa. I don’t taste any quinoa at all in it!

  • Rachel
    December 22, 2017 at 3:47 PM

    What kind of flavors can you use instead of chocolate?

    • Nicole Hunn
      December 23, 2017 at 9:41 AM

      These are chocolate cupcakes, Rachel. It’s not a flavor, it’s really the whole cupcake! You can’t use anything else.

  • Amber
    December 22, 2017 at 2:59 PM

    Definitely going to try this. I’d love to see if maple syrup works for sweetener!

    • Nicole Hunn
      December 22, 2017 at 3:16 PM

      I’m afraid you can’t replace a granulated sweetener with a liquid one, Amber. If you’d like to use an unrefined sugar, I’d try granulated coconut palm sugar. I can’t promise it will work, though, as I haven’t tried it but it’s worth a shot.

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