Healthier Gluten Free Chocolate Cupcakes

gluten free chocolate cupcake with peanut butter frosting and sprinkles

These healthier gluten free chocolate cupcakes truly take the cake! “Healthy” and “Cupcakes” are rarely used in the same sentence; throw “Chocolate” into the mix and it’s a nearly unheard of connection! These cupcakes really do defy the odds.

gluten free chocolate cupcake with bite1

The ingredients in these decadent cupcakes are somewhat unexpected but intentional. Let’s break them down.

Superfood quinoa provides both nutty little crunch of flavor and most of the hidden nutrition for our chocolate cupcake. If you don’t know quinoa, it’s typically used as a side dish like rice (here’s a lovely recipe for gluten free Thai Peanut Quinoa), or sometimes as a gluten free flour, but here it’s part of the dry ingredients in its whole form to add to the structure of the recipe in addition to the gluten free flour. Quinoa is high in protein, fiber, antioxidants, B and E vitamins, magnesium, iron, potassium, calcium and phosphorus. And now it’s in our gluten free chocolate cupcake!

gluten free chocolate cupcake with sprinkles

As for fats, this recipe uses the healthier sorts. These delicious cupcakes can be made soy-free, dairy-free and vegan if you wanna … as coconut oil and some dairy-free sour cream or yogurt are the only fats needed. I’ve also given you plenty of sweetener options so you can choose what’s right for you.

chocolate cupcakes and peanut butter frosting (healthier cupcakes than you might guess, but you'd never know from the taste!)

Unadulterated cocoa powder makes these cakes as chocolatey as you can handle, but choose coffee over milk as an ingredient if you really love chocolate, as coffee enhances the flavor even further!

Hallie with gluten free chocolate spider cupcake

While these delicious cakes need nothing to top them, peanut butter is the perfect complement if you choose to frost them! (Although, my kids informed me that if a cupcake isn’t frosted, it’s called a muffin. Who knew?!) If you’re nut-free, simply opt for a seed butter instead, or of course, you can frost with a standard white or chocolate frosting recipe or try my maple frosting recipe – it would be magic on these gluten free chocolate cupcakes, too!

Remember not to tell the kids (or grown up chocolate lovers) that their treats are healthier than the ordinary gluten free cupcake — they’ll certainly never suspect it on their own!

gluten free chocolate cupcakes spider-chocolate-cupcakes
Turn these yummy healthier gluten free chocolate cupcakes into adorable SPIDER cupcakes by plopping them into spider cupcake holders!


Chocolate + cupcakes are always a good idea. Throw a little extra nutrition inside and a little fun on top, and you’ve got a winning recipe every time! (If you’re looking for some cute spider cupcake holders, here’s a link for you!)


Yield: 12-16 cupcakes, depending on size

Healthier Gluten Free Chocolate Cupcakes

gluten free chocolate cupcake with bite and spoon

“Healthy” and “Cupcakes” are rarely used in the same sentence; throw “Chocolate” into the mix and it’s a nearly unheard of connection! But indeed, these healthier gluten free chocolate cupcakes truly take the cake!

Prep Time 35 minutes
Cook Time 30 minutes
Total Time 1 hour 5 minutes



  • 3/4 cups coconut oil (OR Earth Balance® Coconut Spread OR butter)
  • 1 cup unrefined coconut palm sugar OR maple sugar OR brown sugar
  • 1/2 cup sour cream, dairy or non-dairy OR vanilla or plain yogurt, dairy or non-dairy (I use coconut or almond yogurt)
  • 2 large eggs or substitute
  • 1 tsp pure vanilla extract
  • 1/4 cup pure maple syrup OR agave OR coconut nectar OR date syrup
  • 1 3/4 cups cooked GF quinoa, cold (cook according to package directions)
  • 1/2 cup + 3 Tbs (95 grams) gfJules® All Purpose Gluten Free Flour
  • 3/4 cup unsweetened cocoa powder
  • 2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp salt
  • 1/2 cup prepared coffee OR choice of milk (dairy or non-dairy)

Peanut Butter Frosting:

  • 4 Tbs coconut oil, shortening or Earth Balance® Coconut Spread
  • 1/2 cup natural (no sugar added) peanut butter or other nut or seed butter
  • 1 3/4 cup confectioner’s sugar, sifted
  • 3-4 Tbs milk of choice (dairy or non-dairy)
  • food coloring, optional


Preheat oven to 350° F static or 325° F convection.

Line 12-16 muffin tins (depending on size) with cupcake liners or oil lightly.

Using a stand mixer or large food processor, whip coconut oil and sugar until light.

Add sour cream, eggs, vanilla extract and maple syrup and mix well. Stir in the cooked quinoa and remaining dry ingredients, followed by coffee/milk ingredient.

Mix until smooth -- there will be some texture from the cooked quinoa, but the other ingredients should all be blended at this point. Batter will be spoonable but somewhat thick.

Spoon into lined cupcake tins and smooth tops with a rubber spatula; they should be 3/4 full. Bake for 30-35 minutes – remove when a toothpick inserted into the middle of the cupcakes comes out clean. Remove to a wire rack to cool before frosting.

To make frosting, cream ingredients in a stand mixer or food processor, adding only enough milk for the mixture to achieve spreading consistency.

Or frost with your favorite frosting.


You can also bake this recipe in an 8x8 square pan (like brownies) or an 8 or 9-inch round pan. Line with parchment and bake for 30 minutes or until a toothpick inserted into the center comes out clean.

Here's one option for gluten free chocolate jimmies.

Nutrition Information



Serving Size


Amount Per Serving Calories 392Total Fat 23gSaturated Fat 16gTrans Fat 0gUnsaturated Fat 5gCholesterol 35mgSodium 246mgCarbohydrates 43gFiber 2gSugar 32gProtein 5g

Please keep in mind that nutrition information provided is per serving, which may vary. While we have taken care to provide you with the most accurate nutritional values possible, please note that this information may differ significantly depending on the exact ingredients and brands that you choose to use to make this recipe. Additionally, where options are given for ingredients, the resulting calculation may include ALL ingredient options instead of only one per line, skewing the totals significantly.

Did you make this recipe?

Please leave a comment (and maybe even a picture!) below or share a photo on Instagram! Be sure to tag me! @gfJules

I hope you love this recipe as much as we do!

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Healthier gluten free chocolate cupcakes defy all the odds! Made with healthier ingredients but no less yummy!

healthier gluten free chocolate cupcakes defy all the odds! Made with healthier ingredients but no less yummy!
Gluten Free Chocolate Cupcake Spiders - gfJules

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    • Hi Marie, yes! Just make sure they’re cooled and then you can freeze them in a zip-top freezer bag with the air squeezed out.

  1. Hi Jules, these look amazing! Are these keto diet friendly? I’m concerned about the brown sugar and the maple syrup. And the powdered sugar in the frosting. I hope I can make it work. Thanks

    • Hi Sandra, I’d think that unrefined coconut palm sugar or brown sugar Swerve would work well here. You could also use coconut nectar instead of maple syrup if that helps. Swerve also makes a confectioner’s sugar substitute. I’m not a keto expert, but check to see if those would conform with your dietary needs. Hope so!

  2. Thank You Jules, I can not have Your minx because I cant eat lot of other things, and I will have to change a lot, but I will try, with mine thinks, and hope for the best. This cup cakes looks georges to me too. And I am happy I could copy this recipe, I did not hahto writ it down by hand. Thanks, Antonia.

  3. Hi Jules, I make these yesterday – used the coconut oil – WOW!!!!!!!!!! THESE ARE SOOOOOO MOIST AND DELISHOUS!! (I know delishous is spelled incorrect haha). I was buying these for $3 a pop at a dutch deli – they were awesome also but I didn’t want to keep buying them for $3 a muffin so decided to try my own. Cant wait to try more of your recipes and have signed up for your newsletters? or whatever I’ve signed up for :-). thanks

  4. Sounds delish! I love making your other recipes and have tweaked a few myself to create slightly different and new things! Please know your wonderful Mom told me about you and even gave me a sample, last year when my daughter, her student, was diagnosed. I have been a loyal fan ever since! I love to try out your recipes and always rave about your flour to my GF and non-GF friends! They can never believe the baked yummies I make are GF. Great work Jules!

    • Ah, thanks Heidi! I’ll have to tell her I heard from you – she is pretty wonderful! :) So glad you’re loving my flour and baking yummy treats for your family and non-GF friends! That’s what I love to hear!!!

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