The ultimate sweet deception! Believe it or not, these healthy chocolate cupcakes are 100% whole grain, sweetened with honey and banana, made with coconut oil, and are packed with quinoa and zucchini! That’s right, these deliciously decadent TRIPLE chocolate cupcakes are something you can enjoy without all the guilt! And if you’re trying to sneak in those healthy ingredients without your kids knowing, this Mega Healthy Chocolate Cupcakes recipe is your ticket to success!
Health-conscious parents, the ultimate sweet deception has arrived.
You already know from previous posts that I regularly deceive my children.  Yes, yes, I know.  But it’s all out of love.  I love my family more than anything else in the world and so I like to take good care of them.  Fortunately I don’t have to twist my husband’s arm to eat healthy, he’s fully on board.  My kids on the other hand…yeahhh. It’s a work in progress. And that’s where the deception comes in.
Psssst, come here. Â Look at this cupcake. Â Soft, tender and moist with a glisteningly decadent, fudgy glaze. Â Can you guess what’s in it?
Well I’ll tell you: Â 100% whole grain flour, wheat germ (concentrated nutrients and fiber), coconut oil, raw honey (no refined sugar), an entire cup of quinoa (one of the world’s healthiest grains), a large potassium-rich banana, and a whole cup of zucchini (vegetables, score!).
If someone were simply to describe this concoction to you, you probably wouldn’t feel too excited. But come here a little closer and let me demonstrate how different these cupcakes are.  (*Chomp*)  Just look at the texture.  Can you detect quinoa or zucchini?  Nope!  And the crumb is irresistibly tender and moist.
And the best part, my kids didn’t have a CLUE!
Sweet, sweet deception.
Do you think I watched them devour these with a clear conscience, knowing they were chomping into 100% whole grains, wheat germ, coconut oil, raw honey, bananas, zucchini and getting a mouthful of protein-packed quinoa? Â Heck yes! Â And as soon as they turned their backs I clasped my fingers together and did my evil villain laugh.
“Muhahahahahaaaa!”
And so, dear parents, here’s a healthy treat you can feel good about giving your kids. Â Perfect for dessert, snack, or sending with them to school. Â Just know their teacher may call you with a voice of alarm, “Mr. and Mrs. Wilson, my parent newsletter said a healthy snack.”
Then it’s your turn to grin with satisfaction. Â “Ms. Mumfrey, they are healthy. Â Deceptively healthy. Â Deeeeeliciously healthy!”
Then you can add, “And if you’re a very good teacher to my child this year, I’ll bring you some.”
And of course who said these cupcakes were for kids only? Â These are for anyone who likes sweets but want to enjoy them without all the guilt. Â And so, dear grownups, chomp on!
Healthy Chocolate Cupcakes Recipe
Let’s get started!
In a medium-sized bowl, combine the spelt (or whole wheat) flour, wheat germ, baking soda, baking powder, salt and Dutch cocoa powder.
In a separate large mixing bowl, combine the eggs, honey and coconut oil. Â If the coconut oil isn’t already somewhat liquified at room temperature, microwave it for a few seconds but don’t add it to the eggs while hot. Â Beat the ingredients until combined.
Add the mashed bananas, vanilla, and chocolate cashew milk and beat until combined.
Add the cooked quinoa and zucchini.
Add the flour mixture and fold with a rubber spatula until combined. Â Don’t use an electric mixer for this. Â Fold just until combined, you don’t want to over-stir or the cupcakes won’t rise as well and will be dense.
Stir in the chocolate chips.
Your lusciously healthy batter is ready!
Line a cupcake tin with cups and spoon the mixture in 3/4 full.
In an oven preheated to 350 degrees F, bake for 15-18 minutes or until a toothpick inserted into the center of a cupcake comes out clean.
Be careful not to over-bake or the cupcakes will be dry.
Remove the cupcakes from the pan and allow them to cool completely.
To make the glaze, combine the chocolate, honey, and coconut oil and microwave for a few seconds, stirring occasionally, until the chocolate is melted.
Satiny chocolate gorgeousness! Â It will be runny at first but firms up quickly.
Spread the glaze on the muffins, working quickly because the glaze will firm up. Â If it becomes too firm simply microwave for a few seconds.
If you’re making these cupcakes in advance, wait to glaze them just before serving. Â If you have any leftover, keep them refrigerated so the glaze stays firm.
Enjoy!
Be sure to also try our healthy Chocolate Deception Cake!

Mega Healthy Chocolate Cupcakes
Ingredients
- 2 cups spelt flour (spelt is milder, bakes up softer, and is more easily digested but you can substitute whole wheat flour)
- 1/4 cup wheat germ
- 1/4 cup Dutch cocoa powder
- 1 teaspoon baking powder
- 1 teaspoon baking soda
- 1/2 teaspoon salt
- 2 large eggs (vegan: use liquid egg substitute)
- 1/2 cup honey (vegan: use liquid sweetener of choice such as agave)
- 1/2 cup coconut oil , heat until softened but not hot
- 2 teaspoons quality pure vanilla extract
- 2 teaspoons white vinegar
- 1 cup chocolate cashew milk (can substitute chocolate almond milk or chocolate rice milk)
- 1 large ripe banana , mashed
- 1 cup cooked quinoa (be sure to rinse quinoa thoroughly before cooking to eliminate bitter flavor)
- 1 cup shredded zucchini
- 1/2 cup chocolate chips
- For the Honey Chocolate Glaze:
- 3 tablespoons honey
- 1 tablespoon coconut oil
- 3 ounces semi-sweet or dark chocolate , chopped
Instructions
- Preheat the oven to 350 degrees F. Line two 12-cup standard muffin tins with paper liners (this recipe makes 20 cupcakes).
- Combine the first six dry ingredients in a bowl and set aside. In a large mixing bowl, beat the eggs, honey, and coconut oil until combined. Add the mashed banana, vanilla, vinegar and chocolate milk and beat until combined. Use a rubber spatula to fold the flour mixture into the wet mixture just until combined. Be careful not to over-stir or the muffins won't rise as well and will be dense. Stir in the cooked quinoa and zucchini. Stir in the chocolate chips. Fill the cupcake liners ¾ full and bake for 15-18 minutes or until a toothpick inserted into the center of a cupcake comes out clean. Let the cupcakes cool completely.
- To make the honey chocolate glaze: Place all the ingredients in a bowl and microwave, stirring occasionally, for a few seconds until the chocolate is melted. It will be runny at first but firms up very quickly. Spread on the cooled cupcakes. Work quickly when spreading glaze on cupcakes as the glaze will become firm. If it becomes too firm simply microwave for a few seconds. (Note: If you're making these cupcakes in advance, wait to glaze them just before serving. If you have any leftover, keep them refrigerated so the glaze stays firm.)
Nutrition
Originally published on The Daring Gourmet August 31, 2015
Carol says
I would like to make these gluten-free, and I’m wondering if you think that either coconut flour or almond flour would make a good substitute for the wheat germ. Coconut flour sometimes needs a little additional liquid when substituted for other non-GF ingredients, but it might be all right to just add it to this recipe without any further adjustments due to the water content of the zucchini. What are your thoughts on coconut vs. almond flour? Thank you!
Kimberly @ The Daring Gourmet says
Hi Carol! With it only being 1/4 cup that you’re replacing I think you’ll be fine with either. If I had to pick I’d probably go with almond flour, just my own preference, because the finely ground nuts will likely contribute to a little “lighter” and more delicate crumb than the coconut flour.
Delphine says
Thank you so much for this recipe! I made it several times. It is delicious and super healthy! My kids love it too!!
Kimberly @ The Daring Gourmet says
That’s wonderful, Delphine, thank you!
Veronica says
Hi Kimberly
These cupcakes look delicious! I always bake healthy treats when I bake, but I have never baked with quinoa. I am really looking forward to trying these out! Thanks for posting! :)
Kimberly @ The Daring Gourmet says
Thanks, Veronica! The temperature of the batter, how long it rests and the temperature of the pan all play a role in that. You can experiment with letting it rest longer or in a warmer place or increasing the baking soda a bit.
Jamie says
These look amazing!! I will be making these this weekend with my two year old. One question that might be silly. How do you suggest I cook the zucchini?
Kimberly @ The Daring Gourmet says
Hi Jamie, the zucchini is added raw so no need to cook it. Happy baking!
Jamie says
Thanks for the reply, Kimberly! I made these today with my two year old and they are soooo delicious! We will be making these again and again! One question. Ours didn’t come out super dark and rich like yours INV the picture. They’re a light brown like banana bread. Can you give the weight measurement for cacao? I’m thinking we could have added more. thanks!!!
Kimberly @ The Daring Gourmet says
I’m so glad, Jamie, thank you! It’s roughly 30 grams but the quantity is probably not the reason, more likely it’s the type of cacao powder used – different fat/cacao content. The one I used is probably a darker cacao than the one you used.
Bessie says
Hi Kimberly,
I would love to make these cupcakes. Can I substitute the vanilla extract by vanilla powder? If yes, can you advise me how much vanilla powder? Thank you very much in advance. In the meantime I am going to search how to obtain the chocolate cashew milk here in Holland :-)
Enjoy your day! Bessie
Kimberly @ The Daring Gourmet says
Hi Bessie, yes you can use vanilla powder and I’d probably do a direct substitution (2 teaspoons) depending on how concentrated the flavor is. For the milk you can also use regular milk or whatever you normally use as a dairy substitute. Happy baking and eating! :) Kind regards, Kimberly
Haylie Cox says
Hi Kimberly,
Just wanted to say thank you for the recipe! I tried it tonight and Loved it. I am going to make cupcakes for my daughters first birthday. I started making smoothies to get my son to eat veggies since he started refusing otherwise and now I am trying to sneak anything I can into their food. Anyways, these were delicious!!!! Will be making these again and telling friends!
Kimberly @ The Daring Gourmet says
Fantastic, Haylie, thanks so much!
Tawni says
This is probably a dumb question but does this have a strong coconut flavor? I hate coconut but since trying to go healthy, coconut seems to be a huge ingredient. Is there a different healthy alternative to coconut oil that would work for this recipe?
Kimberly @ The Daring Gourmet says
Hi Tawni, no, it does not have a strong coconut flavor. In fact, I really can’t taste it at all. But if you’d rather not take the risk of being able to taste even a hint of it, you can substitute any oil you like. For example, avocado oil is a healthy oil with a completely neutral flavor.
Kristina says
This recipe looks delicious! I would like to make it as a cake instead of cupcakes, how would you change the recipe to do so? Thank you!
Kimberly @ The Daring Gourmet says
Hi Kristina, thank you! I’d probably go for a 8×8 inch baking pan – same temperature and give it the toothpick test after 20-25 minutes to determine if it needs to bake longer.
Anonymous says
Thank you! I made it yesterday and it needed almost 45 mins in the oven in a round pan (around 9 inches), and in the end there were pieces of zucchini settled in the middle which was less-than appealing to my non-veggie guests (their loss!) lol. I guess I should have raised the temp a bit? However, the flavor was delicious! And I made the cupcake version to send to school for my son’s birthday today :)
Krystalline says
While I love the idea of all of the healthy additions, and am considering making them myself, they are still cupcakes, people! Just counting up the added sugars via honey, in the chocolate cashew milk, and chocolate (but not the sugar from the bananas), these folks who are eating 2 of these glazed cupcakes for breakfast are starting the day with 30 grams of added sugar. :(
Kimberly @ The Daring Gourmet says
Hi Krystalline, clearly these are still a dessert and shouldn’t be viewed as “I can eat as many as I want.” The point here is that they are a healthier alternative to regular cupcakes: 100% whole grain, no refined sugar or vegetable oil, packed with zucchini and protein-rich quinoa, the addition of banana and extra fiber, and for those with dairy issues they’re dairy free.