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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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. :)
Hi, made your chocolate cupcakes for the first time and they were absolutely decadent! My whole family loved them. I can’t believe how dark, rich and moist the cakes were and the frosting was also delicious. I was a bit thrown with the water thin consistency of the chocolate batter but it came out wonderfully. Thank you for this recipe, it will be the only chocolate cake I make. I have a question – did you ever make this recipe with a bundt pan? I have a regular size bundt pan and also a 6 cup smaller bundt (for half the recipe). I’d like to try making the cake in these pans but am unsure of the baking time. Any help with this would be appreciated, we have 2 more birthdays this month!
Thanks again,
Mary
P.S. I just pre-ordered your new book on Amazon coming out next Spring; can’t wait to get it!
Hi, Mary! I’m so happy that the cupcakes came out well for you. :) I’m with you on not wanting to make any other chocolate cake recipes after trying this one! I’ve made this recipe in a 12-cup bundt pan but don’t remember the time. I remember one person saying that they did it for 35 minutes, but that seems quite short (though I could be wrong!) I’d check at 35 minutes and every 5 minutes after that. And I really have no idea about the 6-cup pan but I’m guessing it won’t be that much shorter. I hope that the birthday boys and girls will enjoy the cake! Thanks so much for your feedback and for ordering the book. :)
Yum yum yum… Loved them as much as my kids. I made mini cup cakes though. Kept them for 12 min. They’re a bit sticky… Is it how they r supposed to be or I should have kept them longer? The toothpick had come out clean though.
I wouldn’t say sticky but more like super, super moist and okay… maybe heading in the direction of sticky. ;) If the toothpick came out clean, I’m sure they were done. Thanks for the feedback!
I just wanted to say that this is my go to chocolate cupcakes recipe! I love how they’re so moist, yet still with whole wheat flour. Have you ever tried making a mint frosting for these?
I haven’t tried making a mint frosting! Sounds like something I need to think about for winter time. Thanks for the tip and the rating! So happy that you enjoy the cupcakes. :)
Made a test batch for my 5 year old’s birthday party. Looks like we finally found our cane sugar free cupcake! Will do a kid friendly frosting.
Sehr lecker. Danke! (BTW, he attends a German preschool here in Los Angles, Dad is from Germany.)
I’m so happy that you liked the cupcakes! I hope the kids will enjoy them, too. :) And so neat that your son goes to a German preschool. It’s good to know that such things exist should we move back to the US one day!
Awesome!!
I used 1/2 sugar and 1/2 honey. Also used Coconut oil instead of olive. Healthy never tasted so divine!!!
I’m so happy that you liked the cupcakes, Kathi! And great to know that coconut oil works. I’ll have to try that! Thanks so much for the feedback. :)
I made these cupcakes today,But without frosting. Yummmm. Thanks for the recipe.
So happy that you liked them! Thanks a ton for the feedback and the rating. :)
Any thoughts on how long these will keep? can I make them Thursday night for a Saturday morning birthday party, if I put them in the fridge? I am going to make these for my son’s third birthday party–very excited about the recipe!
That should be fine! They’re very, very moist and last for quite a while. If you’re low on fridge space, store the unfrosted cupcakes at room temperature and then frost them Saturday morning. I hope your son will love them! :)
Thank you so much! I love your blog!
Whoops. Sorry I didn’t see this! Thanks so much, Laura. :)
These were at hit at the birthday party today! I made them Thursday night as planned and then frosted them at the last minute today with sweetened whipped cream–yummy! The birthday boy loved them! and I got 30 out of the recipe, so I’ve had plenty of extras to do taste tests. thanks so much for a great recipe!
I’m so happy that it worked out well! :) And I’m thrilled to hear that the birthday boy liked them too. :) Thanks so much for the feedback!
Oh my goodness, I love you! I was frantically trying to find the perfect healthy chocolate cupcake recipe for a birthday party and I so I decided to go with yours and I am SO glad I did. These cupcakes were BEAUTIFUL. Texture was soooo moist and fluffy, not whole grainy in the slightest. I used Swerve sweetener in place of the sugar. It measures and bakes just like sugar with no aftertaste. This is definitely my new go-to cupcake recipe for sure! The guests at the party were all talking about my cupcakes, they were a hit! Thank you sooooo much! <3
Sorry for the slow reply, Kim! I’m so happy that these worked out with Swerve. That’s awesome. :) And don’t you love it when people are ooh-ing and aah-ing over your healthier baked goods?! Best feeling ever! :D Thanks a ton for the feedback. I really appreciate it! :)
delicious… I made mine with whole grain freshly ground spelt flour, a mix of olive oil, coconut oil and melted butter ( as my olive oil is local and very green and strong tasting), a mix of milk and coconut milk, and a mix of unrefined sugar and rice syrup ( instead of honey, which I believe should not be cooked ).
I also used some melted cooking chocolate mixed in with the wet mix, as I was low on powder.
So many variations from the recipe, but the cupcakes are about as yummy as I have ever made. so rich and moist and fudgey, my kids loved them, I’ll be tagging the recipe… Thanks!
Wow, that’s great that all your subs worked out! I’m so happy that you enjoyed them. :) And adding melted chocolate? Yum! Thanks so much for the feedback! I’ll have to look into the honey thing.
Thank you, thank you, thank you! I have been agonizing over what cupcakes to make for my daughter’s 4th b-day party tomorrow. She wanted chocolate cupcakes with strawberry (pink) frosting. We have cut out all processed foods and so you can imagine the joy I had when finding your blog for whole grain cupcakes! I made the cupcakes today and they were a HUGE hit. She LOVED them and my husband could not tell they were made with whole grain spelt! Fabulous, tender and moist! I halved the recipe and used 1/2 cup of coconut palm sugar and 1/4 cup of local honey and they were great! I will be making another batch tomorrow before the party since I know they are perfect and passed the test from my daughter. Thank you for creating a dessert I feel good about serving my kids and their friends (and myself too, of course) I made a butter cream frosting to go on top made with butter, eggs, honey and fresh strawberry puree to make it pink! Perfect!! Also loved that you put the weight of all the ingredients. SO helpful!! you rock!
First of all, I hope your daughter had a great birthday! I am so happy that you made her these cupcakes and your frosting sounds really nice. And you’re welcome for the weights of ingredients – thank you for saying something about that! You’re one of maybe, 3 people, to have mentioned it. Thanks so much for your feedback and your extremely nice comment! I really, really appreciate it. :) Oh and great to hear about coconut sugar + honey working. I’ll definitely have to give that a try!
I have been looking for a whole wheat cupcake for my daughters party and I came across these…oh my goodness! I made a trail run without frosting since I didn’t have the stuff on hand and we ate 90% of them that night! I did use 1 cup coconut sugar since I was low on regular sugar and they came out amazing! I am excited to do another trail with frosting this time, because…well…I…I mean we, need to make sure they still taste ok ;)
Thank you for sharing this wonderful recipe!!
Haha. I like how you think, Brajee! You definitely need to try out another batch to make sure the frosting is edible. ;) Thanks a ton for your feedback and I hope your daughter has a great party! Oh and it’s great to know that coconut sugar works. It’s now my favorite sweetener but I haven’t gotten around to making these with it. So thanks a bunch for that tip!
Thank you! I am new to this blog and am very impressed. Just made these and have to be the moistest cupcakes I have tried. Truly better than anything you can buy! I did a different icing, with melted chocy and coconut oil as my fiancé isn't a coffee fan. So good :)
Hi Beccy! I'm so happy that you liked the cupcakes. And melted chocolate and coconut oil sounds lovely. :) Thank you so much for leaving feedback and stopping by to say hi. I do love hearing from new readers! Makes my day. :)
Lori – Yay! So happy that you liked them and that the brown sugar worked out. I bet boyfriend couldn't even tell they were whole wheat, could he? :) Thanks for letting me know. I appreciate the feedback!
These are great! I didn't have any white flour on hand, and found your recipe after searching 'whole wheat chocolate cupcakes'. I also didn't have white sugar or enough honey, so I used 1 1/2 cup brown sugar and they turned out fabulous. My bf and I like dark chocolate anyhow so we like it slightly less sweet and more on the rich side. yum.
Rubecca – I don't know because I never use it. Could you maybe try half sugar, half Stevia? I really don't think the consistency will be the same but good luck. :)
Hey Can we use stevia in place of sugar or honey will that make a difference to the consistency of the cupcakes?
Amy – You should definitely try these! But I'd try the sugar version if your family isn't used to whole grain / reduced sugar stuff. When people ask me to make them a cake, I always use the sugar version of this but still use 100% whole wheat and nobody has noticed. Just be careful not to overbake! It loses it's really amazing texture if you do. Good luck. :)
I'm been wanting to make whole grain cupcakes…but afraid no one in the family wanna try it. LOL….silly me. I'm sold on your descriptions. I'm gonna give this a try and just don't mention these are made with whole grain and see what my family would say. I have a thing with the chocolate mocha beans too. Shhh….
Dianne – Wow, thanks! Did you use the honey version or sugar? And if you used sugar, how much did you use? I'd love to hear if it worked with less than what's written. Thanks a bunch for the comment and referring people over here. :)
Great Healthy Recipe!! I love that it uses whole wheat flour and olive oil! Everyone is asking for the recipe and I`m directing them to your website!!
Kathy – To be honest, I think it'd be more like the honey version. And since one cup of honey is supposedly sweeter than one cup of sugar, I'd be worried that it wouldn't be sweet enough. Even with one cup of honey, it was just slightly sweet. I'd be willing to experiment for you on the weekend if you like. Let me know and I'll try it out! :)
I made these cupcakes last night with only 1 cup of sugar and they were amazing. I also used macadamia oil instead of olive oil. My husband couldn’t believe how fudgy and chocolatey they were.
Macadamia oil sounds amazing! I’ll have to look for that. I’m happy you two enjoyed the cupcakes and thanks so much for the feedback! :)
My family is extremely health-conscious, so whole-wheat is great! I was wondering how the cupcakes would turn out with 1 cup of sugar- would it still be gooey, or more like the honey version? Thanks!
FoodEpix – Thanks!
La enredadera – Thanks a bunch! They're not that unhealthy so you can eat one or three. Doesn't matter. :)
bananamondaes – Thanks! I'm happy you found me too. :)
So glad I stumbled across your blog. Great recipe.
I also love the mocha bean, I can only eat one, or two, or three… I have to eat them all!!
The cupcakes (coffe beans or not) looks really cute!! And with that ingredients, they must be really good!!
These cupcakes look so good. Would love for you to share your pictures with us over at foodepix.com.
Nicole – Thanks! I'm so happy people like the mocha beans. Germany never has any cool baking things so I'm super excited to have found something neat. :)
These cupcakes look very, very tasty! I love those chocolate mocha beans on top. I've never seen them before now, but they're such a cute topping for the cupcakes.
Asmita – Thanks! :)
Miryam – It works with 1 1/2 cups of sugar. I wrote that in the recipe but I guess people don't really read the recipe unless they're actually baking them so I'll add it to the description. Thanks for the idea! I bought the beans that way. I found them in the racks at Aldi during "baking week." :)
I think you'd also like the cupcakes with 1 cup of honey. I know honey is still sugar, but 1 cup of honey is better than 1 1/2 or 2 cups of sugar I guess. I just went and ate another one. I promise you wouldn't be disappointed!
These look awesome……just curious to know if you have tried to decrease the amt of sugar before. Do you think they would still be ok with just say 1 1/2 cups? Those coffee beans on top look really good as well did you coat them on cocoa powder or something? Beautiful Picts :-)
What a healthy take on cupcakes. These look gorgeous!!!
Nora – Thanks! I've been planning on trying out some gluten free donuts but I can't find the ingredients anywhere. Not even online! I'm working on it, though. One day I will post something that you could possibly eat should you feel inclined. :)
These look incredible!!! Yum yum, nice job! And your photos are droolworthy…props on using honey,I love using honey as a sweetener :)
Katrina – Thanks. :)
Julie – Thanks! And that's great. One good thing about Germany is that whole grain baking is really cheap here compared to other countries. Thanks for stopping by. :)
Hi there Erin, these cupcakes look like fun. I will follow your site as I am interested in knowing little more about grains and less sugar will not hurt me either. Cheers!
Wowzers, these are lovely! They are so pretty!!
Heidi – Thank you! I really hope you do try them out one day. Please let me know if you do. :)
The cake really doesn't require much work! But if you're referring to taking pictures… I spent almost three hours trying to get a few good shots and ended up with a couple decent ones. I suppose only practice can help that problem. Thanks again for calling my beans non-ridiculous. :)
I'm speechless. These look so incredible! I'm saving this recipe because I know I will use it one day on a special occasion. I can tell how much work you put into this and I am so impressed! And those beans on top look so good – totally not ridiculous :D
Oh well? No! No oh well! :)
The honey version is still super delicious. Maybe I shouldn't have been so critical.
Anything that is described as fudgey, I will eat! Fudgy is my favorite word when it comes to chocolate, but 2 cups of sugar does sound like a lot…oh well!