These gluten-free chocolate quinoa cupcakes were born from my fascination with a chocolate cake recipe made with quinoa and the desire to create a plant-based cupcake version. They are worth trying. And tasty enough you can skip the frosting.
A while back my sister called to say her coworker had brought in a delicious chocolate cake that was made with quinoa instead of flour. I was intrigued. The recipe came from the blog Mel’s Kitchen. I gave it a try and was hooked.
I was on a mission to create a tasty cupcake that used quinoa, was eggless, dairy-free, and didn’t contain white sugar.
Why Plant-Based?
Because I’m always looking for ways to make recipes a tad healthier but still delicious. I like switching up the same old routine for something different. And it’s better for the planet.
Even though I’m not gluten intolerant I have friends who are and after the pandemic hit, I started experimenting with ways to bake without flour, eggs, butter, and milk (which were very hard to find at the time).
After several batches, a couple of adjustments, testing different ingredients, and a handful of food critics (kids and adults alike), I settled on these 3 variations of my gluten-free chocolate quinoa cupcakes. The difference lies in the quinoa and fat used.
Three Variations of Gluten-Free Chocolate Quinoa Cupcakes:
- Quinoa flour and oil
- Cooked quinoa and oil
- Quinoa flour and avocado
Also, the debate is still out on whether to call the quinoa flour version a muff-cake or cake-fin (all short for muffin cupcake or cupcake muffin). It is kind of a hybrid. Or maybe it’s a cup-nie or brow-cake (brownie cupcake). Try it out and decide for yourself. You can definitely enjoy all three without any frosting.
Difference Between Cooked Quinoa and Quinoa Flour
The biggest difference is that one is cooked and the other is toasted and ground to a fine powder. Cooked quinoa has been boiled in water making the seeds fluffy. Whereas, quinoa flour comes from dry, unboiled quinoa seeds. The quinoa is typically toasted and ground to a fine consistency. Similar to all-purpose flour.
You can use either cooked quinoa or quinoa flour for these cupcakes.
The biggest difference I found was during the mixing stage and with the end result.
During the mixing stage, you’ll need to put the cooked quinoa in a blender to create a smoother consistency. This is important as you don’t want a weird texture to your cupcakes. You’ll essentially add all of the wet ingredients together in the blender and mix well.
The cupcakes made with cooked quinoa come out moister but take longer to cook. They also have a deeper chocolate taste (almost like dark chocolate).
The cupcakes made with quinoa flour are drier but take less time to cook and are easier to frost. They have a good taste to them as well. During the mixing stage, you’ll combine the quinoa flour with the other dry ingredients and then add the wet ingredients.
WHERE CAN YOU BUY QUINOA FLOUR OR QUINOA?
Most grocery stores carry quinoa flour and quinoa. You can find quinoa flour in the baking aisle with the other flour varieties or in the specialty foods section.
Quinoa is typically found in the bean and rice aisle or again the specialty foods section. Be sure to purchase white quinoa for this recipe as quinoa comes in different colors.
HOW MUCH QUINOA DO I NEED TO COOK?
Quinoa typically quadruples when cooked. Meaning if you start out with 1 cup of dry quinoa you’ll end up with about 4 cups cooked. For this recipe, you can use 1/2 cup of dry quinoa (1 cup water) and then once cooked, measure out 1 cup. Save the rest for a side dish.
Be sure not to pack the cooked quinoa when measuring out a cup for the recipe. Use a spoon to fill up a measuring cup.
HELPFUL TIPS:
- Always rinse your quinoa well in a strainer before cooking. This helps significantly reduce the bitter taste commonly found with quinoa.
- To cook add 1/2 cup of rinsed quinoa and 1 cup water to a pan. Bring to a boil. Then simmer uncovered for about 15 minutes. All of the water should be gone. Be careful not to burn the quinoa.
Canola Oil vs Avocado
Most cupcake recipes call for butter. However, replacing butter with canola oil or avocado cuts down on the saturated fat content.
I decided to give avocado a try as I find it’s really tasty in other chocolate dessert recipes that I make. The texture reminds me of butter and it provides an array of health benefits.
If you decide to use avocado be sure to get one that is ripe (soft).
Both the avocado and oil variations turned out very similar with only a slight taste difference. The cupcakes that contained avocado had a more chocolatey taste. Baking time was the same. In terms of a crowd-pleaser, it was a tie among my taste testers (adults and kids included).
I encourage you to use what you have in your pantry or fridge. And eventually, give both a try. You can decide which one you and your loved ones prefer.
Honey is a great substitute for white sugar
I’ve become less and less of a fan of using white sugar in recipes. Anytime, I can substitute honey, I’m all about it.
Now first things first. Sugar is sugar. At the end of the day no matter which way you look at it, white, honey, maple syrup, dates, etc. are all a form of sugar.
The difference with honey? More nutrients and you can use less of it.
Unlike white sugar, honey has some healthy nutrients and benefits. Plus, you can get away with using less of it without sacrificing the sweetness because honey tends to be sweeter than white sugar. That means less overall sugar content, more nutrients, and still a great taste.
Use Flax Eggs for Omega-3s and Fiber
Another great way to up the nutrient content, especially Omega-3s and fiber, is to use flax eggs in place of regular chicken eggs. My go-to flax egg recipe is beneficial to have on hand when it comes to baking.
Plus, if you ever run out of eggs it’s nice to have a quick and easy substitute that will get the job done.
Whipped Chocolate Frosting (with a dairy-free version)
Although you can enjoy these cupcakes without frosting, here are two quick whipped chocolate frostings to try.
Heavy Whipping Cream and Semi-Sweet Chocolate Chips
- 2 1/4 cups heavy whipping cream
- 1 1/4 semi-sweet chocolate chips
DIRECTIONS: Bring whipping cream to a simmer on the stove on medium heat. In a glass bowl, pour whipping cream over chocolate chips. Let sit for 5 minutes and then stir until glossy and smooth. Cover with plastic wrap and place in the refrigerator for 2-3 hours.
Then with a hand or stand mixer whip the frosting to soft peaks. Firm yet soft enough to pipe.
Coconut Cream and Semi-Sweet Chocolate Chips (Dairy-Free)
- 3/4 cups coconut cream
- 1 1/2 semi-sweet chocolate chips (naturally dairy-free)
DIRECTIONS: Chill a can of full fat coconut milk in the fridge for 2-3 hours. Open and scoop out the firm cream.
Use the double-boiler and place chocolate chips and coconut cream in a glass bowl over a pan of boiling water. Stir constantly until the chocolate and cream fully melt. Remove and let cool slightly. Cover with plastic wrap and place in the refrigerator for 2-3 hours.
Take out of the refrigerator and let warm up for 10-15 minutes. Then scoop chocolate away from the sides or scoop the chocolate into a stand-mixer. (If keeping in the original bowl you can use a hand-mixer.)
With a whisk attachment, whip the chocolate and coconut cream until the frosting turns to a lighter milk chocolate color. The frosting should be firm enough to not be a liquid but soft enough to pipe.
Did You Make This Recipe?
Please let me know what you think. Leave a comment and star rating below. Also, be sure to share a picture of your creation on Instagram and tag #megansophiewellness. I love to see what you make!


Gluten-Free Chocolate Quinoa Cupcakes (3 variations)
Ingredients
QUINOA FLOUR WITH OIL OR AVOCADO
Dry Ingredients
- 3/4 cup quinoa flour
- 1/2 cup cocoa powder, unsweetened
- 1 teaspoon baking powder
- 3/4 teaspoon baking soda
- 1/4 teaspoon sea salt fine (I use Real Salt)
Wet Ingredients
- 2/3 cup honey
- 1/3 cup canola oil (OR use a full 1/3 cup of mashed avocado)
- 1/3 cup almond milk, unsweetened
- 2 flax eggs (See
flax egg recipe ) - 2 teaspoons pure vanilla extract
Add at the end
- 1/4 cup mini chocolate chips (semi-sweet)
COOKED QUINOA WITH OIL
Dry Ingredients
- 1/2 cup cocoa powder, unsweetened
- 1 teaspoon baking powder
- 3/4 teaspoon baking soda
- 1/4 teaspoon sea salt fine (I use Real Salt)
Wet Ingredients
- 1 cup cooked quinoa (White)
- 2/3 cup honey
- 1/3 scant cup canola oil (about 1 tablespoon less than full)
- 1/3 scant cup almond milk (about 1 tablespoon less than full)
- 2 flax eggs (See
flax egg recipe ) - 2 teaspoons pure vanilla extract
Add at the end
- 1/4 cup mini chocolate chips (semi-sweet)
Instructions
- Preheat oven to 325°
QUINOA FLOUR WITH OIL OR AVOCADO
- Combine and mix all dry ingredients. Set aside.
- Combine all wet ingredients and using either a fork or hand mixer, stir together until fully combined. Be patient. The honey starts out thick but eventually will thin out. (If using avocado be sure to thoroughly mash separately beforehand. Can also use a mixer or blender to get a smoother consistnecy before adding to the other wet ingredients)
- Add the wet ingredients to the dry and combine until almost fully mixed. Then add chocolate chips and mix well.
- Fill muffin pan cups about halfway full (about 1/4 cup)
- Bake for 19-23 minutes until a toothpick inserted comes out clean.
- Let cool in the pan for 5 minutes.
COOKED QUINOA WITH OIL
- Combine and mix all dry ingredients. Set aside.
- Add all wet ingredients to a blender and mix until smooth. (This step is important to smooth out the texture of the quinoa).
- Combine the wet ingredients with the dry. Mix until almost fully incorporated. Add chocolate chips and mix well.
- Fill muffin pan cups about halfway full (about 1/4 cup)
- Bake for 30-34 minutes until a toothpick inserted comes out mostly clean. (May have some chocolate on the toothpick as this version is slightly more mosit)
- Let cool in the pan for 5 minutes.
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