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!
7 comments are awaiting moderation!
Hi Erin,
Your recipe sounds fab. Its my moms birthday tomorrow. I wanna do these lovely cupcakes for her. Unfortunately enough she can’t eat eggs. Any substitute you can suggest?
Thanks
Prity
Hi Prity! Thanks. :) I haven’t tried any egg subs in these, sorry. I normally use chia eggs but since I haven’t tried them in these, I can’t say for sure if it’d work.
I made these tonight and they are probably the best cupcakes I’ve ever made!! Just out of curiosity, why the need for boiling water? I like to learn the reasons why for to learn. 😊
Woohoo! So happy that you liked them so much. :) I had no idea what the answer was so I googled it and found this, which has some ideas. Thanks for your feedback!
I’ve made these cupcakes several times and they are so good I’ve made them my staple chocolate cupcake recipe. They’re so good I eat them by themselves without frosting. I’ve made batches with less sugar and 1 1/2 c. of sugar are my preferred amount, but 2 c. of sugar isn’t too sweet either. The are really moist and the pourable batter actually makes it easier to handle for me. Easy and delicious. This is the first recipe I’ve made from ou and I look forward to making more.
Yay! I’m happy to hear that they’re your staple cupcake recipe and that you’ll be trying more of my recipes. :) I hope you’ll enjoy them just as much as these cupcakes! Thanks for your comment.
Thank you so much for the recipe!
You’re so welcome! I’m happy you seemed to have liked them. :)
Thank you Erin for this recipe! I made them for the first time for my little guy’s fifth birthday today. I am doing the honey version. I just took them out of the oven and I am amazed at how they actually rose and baked from such a thin batter!! I have this strong feeling we will be making these again…take care!!
I hope that they were enjoyed at the party and that your son had a great birthday! Thanks a bunch for your comment. :)
Can I bake this in a 8 inches cake tray?? Loove for this recipe..I have been searching for a whole wheat chocolate cake recipe sweetened with honey
You can use two nine inch round pans and bake for 30-35 minutes. :) Or you can halve it and use an 8″x8″. I’m not sure of the baking time. Hope you’ll enjoy it!
The cake came out really well and I used honey. Do post more recipes using whole wheat and honey as sweetner. I will definitely make many more of this cake.Want everyone to taste it. No one who had could guess its made of whole wheat and honey!
I’m so happy that it was a hit! I also like whole wheat + honey. :) You should try these whole wheat cinnamon apple muffins next! They’re also honey sweetened and super yummy.
Love love love these. Used agave nectar.
Moist and fluffy. Amazing!!!
❤️❤️❤️❤️❤️
Aww, yay! I’m so happy that you enjoyed them! Thanks for the tip on agave and your comment. :)
Hi, can I use 1 cup of coffee instead of the water? I want to make this cake for my son’s birthday and want to know if this will rise enough with whole grain whole wheat king Arthur flour? Thank you in advance.
Hi there! That would work and should be quite tasty. :) I haven’t tried that specific brand of whole wheat flour in this exact recipe but every other brand I’ve tried works just fine!
Thank you so much. I will let you know how it turns out.
Sooooooooo yummy and moist! I used King Arthur whole wheat flour, 1 1/2 cups of sugar instead of 2 and added chopped walnuts to my batter. They were delicious!!!!!!
Yum! Chopped walnuts sounds like a great addition. :) I’m thrilled that you liked them so much! Thanks a bunch for your comment. :)
Claims that this is the best gluten-free chocolate cake ever are NOT over rated. I have made this recipe several times and each time, the cupcakes are fantastic.
For Canadian readers, I use Bulk Barn’s 1:1 gluten free flour mix (in place of Erin’s suggested Bob’s Red Mills) and the results are great. I also freeze any leftover cupcakes 24 hours after baking. The flour I use takes on a faint “beany” under-taste on day 2 that slowly increases as days go by. Freezing prevents this.
Wow, thanks! I’m thrilled that you like them so much. :) Thanks again for leaving the tip for the Canadian readers! I’m sure that’ll help others. And good to know about the beany taste and freezing them! Thanks for your two comments today. :)
I think I need to do some baking today. These look delicious, I’ve been craving sweet things lately and this will fit the bill perfectly.
I think you do, too. ;) I hope you’ll enjoy them! They should definitely satisfy your sweets craving. Thanks for your comment!
hi :-) can I use natural unsweetened cocoa/hershey’s cocoa powder for this recipe? thank u
Sure! That’ll work fine. I just prefer the darker kind. Enjoy! :)
I love this idea for a kids’ birthday party! Healthier but not quite the texture of paleo baked goods is perfect for little ones (and adults alike)! YUM!
Thanks! I bet little ones would like my paleo cupcakes, too. ;) But it’s hard to compete with wheat!
YUM!! I love using whole wheat and spelt. You are right the weight measurements can make a difference. When I tested those recipes for your cookbook I did one by cups. I had ground my own wheat and it was so light and airy it was not enough flour. It didn’t turn out so good. Then I weighed the flour and it was a big difference. Might not have been so much had I not just ground my own instead of using store-bought.
Exactly! It’s super important to weigh your ingredients and especially when you grind your own flour. :) I hope you try these! I bet you’d love them. :)
Made these for a family bbq on Saturday and finished them off on Wednesday and they were JUST as moist and delicious. Can’t wait to try some of your other recipes!
Wow, they lasted a long time. :) That’s great. And I’m happy they were enjoyed at the BBQ! Thanks for your comment.
The best chocolate cake I have ever baked. Moist, rich, and full of goodness.
Yay! I’m so happy you liked it. Thanks for your comment!
Best recipe ever!! I used water instead of milk and a tad less sugar. Sooooo good. I made a quadruple batch and it was GONE in 2 days. Thank you!
Woohoo! I’m so happy that you liked them. :) Thanks for your comment!
Amazing texture and totally loved it..thanks for a recipe.
Awesome! I’m happy they came out well. Thanks for your feedback!
I dont have cocoa powder, can I sub it with dark chocolate bars in anyway? Thanks…
That unfortunately won’t work. You really need cocoa powder for this recipe! Sorry about that.
Hi Erin, out of curiosity,,,will the eggs not get scrambled in boiling water?
They won’t! Promise. :)