These 100% whole wheat chocolate cupcakes are made just a little healthier with less sugar (or honey!) and are incredibly moist. Can also be made with all-purpose or gluten-free flour and they’re naturally dairy-free.
I first posted this recipe almost 5 years ago. It’s my favorite chocolate cake or cupcake recipe and it’s ruined almost all other chocolate cake recipes for me. They’re never moist enough.
I do love my paleo chocolate cupcakes but they have a totally different texture and they can’t really be compared.
I thought I should try making this whole wheat recipe gluten-free so I tried them first with buckwheat. That resulted in some funky weirdness. They tasted… floral.
So then I tried them with Bob’s Red Mill gluten-free 1-to-1 baking flour and they worked perfectly! If you use that, I really recommend going by the weight I list in the recipe rather than using measuring cups. I always recommend that, but especially when it comes to gluten-free flours. :)
For another delicious cupcake recipe using that flour mix, try these gluten-free vanilla bean cupcakes from Gluten-free Palate!
There are two ways you can make these cupcakes when it comes to sweetener: with sugar or with honey. The texture using sugar is mind-blowingly awesome. It’s the moistest chocolate cake ever. Kind of fudgy, even. Pretty much everyone who tastes this cake says it’s the best chocolate cake they’ve ever had.
The version with sugar is, in my opinion, tastier than the honey version, but with two cups of sugar, which the original recipes calls for, it’s kind of ridiculous. It also works with 1 1/2 cups sugar (but it’s even yummier with 2 cups!).
For another delicious whole wheat and honey recipe, try my whole wheat apple muffins! They’ve always been a big hit.
The honey version is almost as good. I used one cup of honey instead of two cups of sugar and it’s pretty awesome.
The taste is almost as good as the two cups of sugar version but the texture is like normal chocolate cake, and not like the super duper moist and fudgy original recipe. I’m thinking with the frosting, nobody would even notice.
And if you’re wondering if you can taste the whole wheat in these whole wheat chocolate cupcakes – definitely not! I’ve made them dozens of times and when I decided to replace all of the white flour with whole wheat (or whole spelt), nobody noticed. The gluten-free version also tastes the same as the all-purpose flour version.
I used this healthier cream cheese frosting to top these cupcakes off but this vegan chocolate fudge frosting would also be great! So would this chocolate cream cheese frosting.
And for a great chocolate + strawberry treat, this strawberry buttercream frosting looks amazing.
These cupcakes would also be the perfect base for these super cute bear cupcakes. :)
That’s it! If you try the cupcakes, I’d love to hear what you thought. Thanks! :)
100% Whole Wheat Chocolate Cupcakes (dairy-free with gluten-free option)
- Prep Time:
- Cook Time:
- Ready in:
- Yield: 24 cupcakes
Ingredients
- 2 cups (400 grams) granulated sugar or raw sugar or 1 cup (320 grams) honey1
- 1 3/4 cups (210 grams) whole spelt, whole wheat flour, white whole wheat flour, all-purpose flour or 1 3/4 cups (236 grams) Bob's Red Mill 1-to-1 gluten-free baking flour
- 3/4 cup (85 grams) Dutch-process cocoa powder
- 1 1/2 teaspoons baking powder
- 1 1/2 teaspoons baking soda
- 1 teaspoon salt
- 2 eggs
- 1 cup (240ml) milk of choice (but not canned coconut milk)
- 1/2 cup (120ml) olive oil (or canola oil or another neutral tasting vegetable oil that's liquid at room temp)
- 2 teaspoons vanilla extract
- 1 cup (240ml) boiling water (I know that sounds like a lot but I promise you, you need 1 cup!)
- 1 batch healthier cream cheese frosting (which is what I used on these - that recipe is enough for 4 teaspoons on each cupcake) or 2 batches vegan chocolate fudge frosting (for a dairy-free option - use 4 teaspoons of frosting per cupcakes)2
Cupcakes:
For the frosting:
Directions
- Preheat your oven to 350 °F (175 °C). Line 2 muffin pans with 24 liners.
- In a large bowl, stir together the sugar (if using honey, don’t add it yet), flour, cocoa, baking powder, baking soda and salt.
- Add eggs, milk, honey (if using), olive oil and vanilla.
- Mix for 2 minutes on medium and then stir in the boiling water. The batter will be almost as thin as water.
- Fill each liner just a little more than halfway full.
- Bake for 14 – 18 minutes or until a toothpick comes out with some moist crumbs, but no liquid. If you make the gluten-free version, you'll need closer to 18 minutes. If you make the whole wheat / all-purpose versions, you'll need more like 14-16 minutes.
- Let cool for 5 minutes in the pans, and then turn out onto a rack to cool. Let cool completely before frosting.
Notes
- I’ve also used 1 1/2 cups sugar and it was still sweet enough.
- Here is the original frosting recipe I had listed on this recipe:
– 1 cup (240ml) whipping cream
– 1 8-ounce package (225 grams) cream cheese
– 3/4 cup (98 grams) powdered sugar
– 1/2 teaspoon espresso powder
– 1/2 teaspoon vanilla
Beat the whipping cream until stiff peaks form.
In a separate bowl, using the same beaters, beat the cream cheese until soft and smooth. Slowly add the powdered sugar.
Dissolve 1/2 teaspoon of espresso powder in 1/2 teaspoon vanilla (I did this in a tablespoon). Add this to the frosting. If you want more coffee flavor, keep adding 1/2 teaspoon espresso / vanilla until you’re happy.
Fold in the whipped cream and frost the cooled cupcakes. Store frosted cupcakes in the refrigerator.
Adapted from One Bowl Chocolate Cake
Note: The pictures were updated in September, 2016.
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213 comments on “100% Whole Wheat Chocolate Cupcakes (gluten-free, all-purpose options)” — Add one!
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Hi Erin,
Thanks for the recipe. I made the cupcakes this afternoon and they turned out delicious! I grow some chocolate mint in my backyard so I decided to sprinkle some shredded leaves in the batter (yum!). I didn’t make the frosting, but sprinkled some chocolate chips on top. Double yum! This one is a keeper. Thanks again!
Hi Yany! I’d love to try these with chocolate mint. That sounds delicious. :) Thanks for the tip and for your comment! I’m so happy that you enjoyed them. And my apologies for the slow reply! I just got back from vacation and wasn’t able to access the page from my laptop where I approve and reply to comments. Sorry again!
Hi again Erin! Not a problem. Hope you enjoyed your vacation! I am trying another of your recipes today (the zucchini chocolate brownies)… Can’t wait for them to come out of the oven… I am trying to keep my baking to once every two weeks or so, but it’s so hard with all these yummy recipes. Keep them coming! :)
Hi there! I did indeed, thanks. :) And ooh… I hope you enjoyed the zucchini brownies! Those are a favorite of mine. Thanks a bunch for your nice comment! :)
This is my favorite chocolate cupcake recipe!! Could it be made it into a cake?
So happy you like them! They’re my favorite chocolate cupcakes / cake ever. You can bake these in two 9-inch pans for about 30 minutes. Maybe check at 25 minutes to be on the safe side. I mentioned you in my latest post! Did you see? :)
I did see that! I made this recipe in a 13×9 and baked it for 30 minutes. I used my KoMo to mill fresh white wheat! Turned out great, just like the cupcakes.
Happy Birthday to me!
I hope you had a great birthday! And thanks for sharing the baking time for a 9×13. :)
Made these and they are the most delicious thing i have ever baked in my whole life! For the cupcakes I used whole grain spelt for the flour, 1 cup of maple syrup in place of the sugar, cacao instead of cocoa and for the frosting i used 1/3 cup maple syrup instead of the sugar, doubled the vanilla and omitted the coffee powder. So easy to make.
Wow! I’m thrilled that you enjoyed them so much and I love your healthy subs. :) Especially the switch to maple syrup! I’ll have to try that next time. Thanks a bunch for your feedback!
Absolutely delicious (cooked and raw! – couldn’t keep my fingers out of the bowl!) I made it with 1/2 cup coconut sugar, 1/2 cup white sugar and 1/2 cup agave nectar. Also I used Chapati flour and it turned out amazing! Will definitely make this again as I doubt the 24 cupcakes and 6 Madeleines will last too long in my house.
Haha. I love the batter, too! I’d never heard of Chapati flour before but it sounds interesting. I’m so happy you enjoyed the cupcakes! Thanks a ton for your feedback. :)
I found this recipe last week and have already made two halved batches of the cupcakes using sugar(not the icing-I went for chocolate on chocolate). Absolutely delicious. Thank you!
I’m so happy you enjoyed them! You can never go wrong with chocolate frosting on cupcakes. ;) Thanks for your feedback!
The cupcakes were moist. The batter was runny looking but it all worked out. I did not use the icing either. I substituted honey for sugar. I might add more honey next time.
It’s supposed to be runny, almost like water, so the batter was fine. :) I’m happy you enjoyed the cupcakes! Thanks for your feedback.
Erin, you struck gold! …And now so have I. I thought I would never be able to fully enjoy another chocolate cupcake without stressing over the processed and refined ingredients within. I made your cupcakes (the honey version) exactly as instructed and they came out perfectly! They were moist, springy, and heavenly. Not sure where people are getting the sticky outcome from. My cupcakes did sort of glisten, but were by no means sticky. I used 100% whole wheat pastry flour and I only had to bake for 14 minutes. I used extra virgin olive oil, though I was really tempted to use coconut oil instead (especially since someone else used it successfully), however I try not to steer away from a recipe the first time I make it ESPECIALLY when it comes to baking. Great recipe! This is definitely a keeper!
Oh, I forgot to mention that I did not make the icing. It had a couple of ingredients in it I was not comfortable with (i.e. cream cheese and powdered sugar). I will keep searching for an icing recipe, however these were great without any icing.
I don’t like the powdered sugar, either. :( But I’m with you – I like these even without the icing!
I think only one person mentioned the sticky thing and I kind of know what they mean. They’re not sticky really but ultra moist and like you said, they glisten. :) And that’s awesome that you like to follow the recipe the first time you make it! Most of my readers seem really good about that but I read so many comments on other blogs saying that they changed every other ingredient and the end product was the worst XYZ they’d ever had. I wonder why. ;) Thanks a ton for your feedback! I’m so happy that you enjoyed them.
Tried out this recipe for my birthday last weekend; used honey (trying to cut down on refined sugars in my diet) and they were a total hit! I will definitely be trying out more of your recipes; I love that there’s multiple healthy adaptations/substitutions :-)
Thank you! It’s good to know that the options are appreciated. :) I’m so happy that these came out well for you. Thanks a ton for your feedback and I hope you had a great birthday!
That was the wonderful cake it turned out to be. Thanks for giving a healthy bite. one question though. It is little sticky.. is it supposed to be like that? otherwise it was just awesome.
A little stick sounds about right. You could bake it a little longer to see if that makes it less sticky! Thanks for your feedback. So happy you liked the recipe!
Hey,
I made it again and this time it was perfect ? .
Just wanted to know one more thing , can we make vanilla cupcake also with wheat flour ?
If yes then plz let me know the ratio of all ingredients.
Thanx a lot ?
I’m happy that they worked this time! I knew something had to be wrong last time. :) You can make vanilla cupcakes with whole wheat flour but not using this recipe. For that, you’d need to google “whole wheat vanilla cupcakes.” Good luck on your next whole wheat attempt. :)
Hey
Yesterday i made this chocolate cupcake. it took more then half an hour (around 45 minute) to bake it completely. And the final result was good but not satisfied. Cupcake top was very hard and inside little sticky sticky. Plz suggest me what should i do. Thanx ?
Hello! Did you make any changes at all to the recipe? If you didn’t, then perhaps your oven is off because these cupcakes (and all other cupcake recipes) don’t take anywhere near 45 minutes to bake. I’ve made this recipe at least 20 times and never had them take longer than 17 minutes. And it looks like none of the other reviewers had issues with them, either. If you used an oven thermometer to ensure that your oven isn’t running low, then you must have accidentally added too much liquid. Just yesterday I made some cupcakes and wondered why they weren’t rising. I had forgotten the baking powder! Mistakes like that happen to everyone. ;) I hope you try again because they’re really delicious!
Just made these, they are delish, made a different frosting. Don’t forget to sift the cocoa powder, so you don’t get little bits of clumped chocolate.Thnx for sharing your recipe.
I’m happy you liked them! Thanks for your tip and feedback. :)
Just made these and I reduced the sugar to only one cup. But Then I started worrying they wouldnt be sweet enough and threw in 3 packets of stevia, lol. They turned out great! Very moist! Will make again. Thanks for the recipe.
I love reducing sugar when possible but I probably wouldn’t halve the sugar in a recipe unless you want it to come out very differently than the original recipe. ;) I’m happy it worked with some added stevia! Thanks a bunch for your feedback.
I just got done making these but I subbed the whole wheat flour for the Krusteaz one-for-one gluten free wheat flour and they came out so well! I love to bake cupcakes but have a friend who’s gluten free and I’m so excited to be able to include her. Thank you!!!
That’s so nice of you to bake something gluten-free for your friend! I hope she’ll enjoy the cupcakes. :) Thanks so much for the tip on making these gluten-free and for your feedback!
so if i wanted to add vinegar in this sort of make a whole wheat red velvet what would u recomend? should i sub buttermilk for the milk and add vinegar to soda?
There’s so much cocoa powder in these that red velvet wouldn’t work (red velvet cakes have much less cocoa powder). And adding vinegar, buttermilk and baking soda to the recipe would require totally reworking the recipe so the easiest thing to do would be to find a red velvet cake recipe and just use white whole wheat flour. :)
Are your grains freshly ground? Can I substitute applesauce for the oil?
No, they’re not. Please go by weight if you want to use freshly milled flour. I’ve never subbed applesauce for oil in these cupcakes but I wouldn’t recommend subbing all of it. Maybe 1/3? But again, I haven’t tried it so it’s just a guess!
Can I use cocoa powder instead of espresso powder?
I haven’t tried that but it may work. If I were you, I’d just omit the espresso powder. No need to sub anything in for it. :)
Isn’t espresso a type coffee? If I’m correct, what can I use in it’s place? I hate coffee.
You can just omit it. :)
I made these for my twin daughters’ second birthday, and they were a hit! I modified them a little: used 1/2 c. coconut sugar and 1/2 c. honey; used coconut oil; soaked the pastry flour overnight in a mixture of yogurt (couple tablespoons) and coconut milk to sub for the 1 c. of milk. They were great–moist and sweet enough without frosting. (I did drop a few chocolate chips in each cupcake of the second dozen.)
So modifying the recipe for soaking the grain (as per Nourishing Traditions) works well! I just added the wet goods to the soaked grain, mixed the cocoa powder with the leavenings and salt and then added that in, and then added the boiling water last of all.
Thanks for a great recipe!
I love that you soaked the flour first and that it worked out! I need to try that. I’ve always been hesitant to try and I have no idea why. Thank you so much for the tip and your feedback! I hope your daughters had a great birthday. :)
Hi, second attempt at ur cupcakes.. Super yumm.. Only issue.. They spilled from the moulds and didn t get a round top.. Did I over mix?
It sounds like maybe the liners were filled a little too much. Next time, fill them a little less and see if that helps. You won’t get much of a dome with these cupcakes but they shouldn’t spill! I’m happy you enjoyed them. :)