100% Whole Wheat Chocolate Cupcakes (gluten-free, all-purpose options)
These 100% whole wheat chocolate cupcakes are made just a little healthier with less sugar (or honey!) and are incredibly moist. They can also be made with all-purpose or gluten-free flour, and are 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 it 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. :)
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 recipe 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 regular chocolate cake, and not like the super-duper moist and fudgy original recipe. I’m thinking that 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 – you can’t! 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, 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. :)
100% Whole Wheat Chocolate Cupcakes (gluten-free, all-purpose options)
Ingredients
Cupcakes:
- 2 cups (400 grams) granulated sugar or raw sugar or 1 cup (320 grams) honey
- 1 3/4 cups (210 grams) flour see notes
- 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 50 grams each out of shell, room temp
- 1 cup (240 ml) milk of choice but not canned coconut milk
- 1/2 cup (120 ml) neutral oil canola, vegetable, light olive oil
- 2 teaspoons vanilla extract
- 1 cup (240 ml) boiling water not a typo!
For the frosting:
- 1 batch healthier cream cheese frosting
Instructions
- 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.2 cups (400 grams) granulated sugar, 1 3/4 cups (210 grams) 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
- Add eggs, milk, honey (if using), olive oil and vanilla.2 eggs, 1 cup (240 ml) milk of choice, 1/2 cup (120 ml) neutral oil, 2 teaspoons vanilla extract
- Mix for 2 minutes on medium and then stir in the boiling water. The batter will be almost as thin as water.1 cup (240 ml) boiling 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
- For the flour you can use, 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 for a gluten-free version.
- For the 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).
- I’ve also used 1 1/2 cups of sugar, and it was still sweet enough.
- Here is the original frosting recipe I had listed on this recipe:
- 1 cup (240ml) heavy 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.
- The nutrition information provided is calculated as a courtesy and is only an estimate. I am not a licensed nutritionist or dietitian. For the most accurate nutritional data, consult a professional or use your preferred calculator. The values are without the frosting.
- Adapted from One Bowl Chocolate Cake.
Hey
It’s a nice recipe
Did you just use whole wheat flour or it was mix of all purpose flour and wheat flour
Hi again! I replied to this via email but in case anyone else is wondering, you can use 100% whole wheat or 100% AP flour or any combination of the flours listed. :)
YUMMYYYY!!!!!
This recipe tasted soooo good! I used jaggery and honey and it still worked! I made a cake and 7 cupcakes with the batter and it was soo good. EVERYONE loved it!! I will make this again. Instead of the frosting, I made a glaze out of powdered sugar and milk. Mmmmmmmmmmmmm
Thanks for the tip on jaggery! I’ve never tried that. I’m so glad that it worked well and that you liked it! Thanks for your comment. :)
I tried so many while wheat sugar free muffins, and this was the best, absolutely perfect. Thank you for the recipe dear. But can i substitute cocoa powder for more flour and make it vanilla cake?
I’m so happy you liked them! But unfortunately you can’t make this into a vanilla cake. :( The whole recipe would need to be reworked. Sorry about that!
I was putting big hopes I can do that :( unfortunately, so do you know another recipe for vanilla cake with whole wheat flour and sugar free, I can use honey or maple syrup as a sweetener.
Sorry but I don’t. I’ve never had a good healthy vanilla cake. :(
Hello erin :)
I wanted to ask you if I could use liquid jaggery if I don’t have honey.
Hi there! I’ve never actually used that so I really don’t know. Have you used it in place of honey before? If so, I bet it would work. Enjoy. :)
Hello Erin,
Thanks for sharing this absolutely delightful recipe. I use the exact same proportions and baked a very chocolaty and moist cake instead for picnic with our friends today. I also added some choco chip and the cake was mind blowing !
The only issue I faced was that my microwave oven wouldn’t set to the exact temperature – it’s either 170 C or 180C, so I kept it at 170 and baked the cake for a total of 55 mins.
Hi there! You’re welcome for the recipe. :) I’m so glad that it worked out well at a different temperature and in cake form. And added chocolate chips are always a good idea. :D Thanks for your feedback and my apologies for my very slow reply!
Wohoo, i just have to make them for my mothers birthday this week after reading so many positive comments! :)
I just wonder if I can use erythritol instead of sugar? Cause some of us are alergic to sugar and honey. :) Normaly I use it in most of my baking but just want to be sure for this, cause I’ll be making a muffin tower and need a lot of them. ???? Thank you and wishing you a magical week! ????
I’m so sorry for just now seeing your question! Especially since it was for your mother’s birthday. :( I don’t use erythritol (it gives me gut issues) so I really don’t know. Can you use maple syrup? I think that would work. Sorry that I can’t be more helpful and I’m really very sorry again for my slow reply. I’m not usually this bad!
Hi!
I made these yesterday and they came out so well! Super moist and pretty. Everyone in the house loved it. I couldn’t find baking soda, hence used baking powder 4 times the required amount of baking soda (in total 7.5 teaspoons). Also for the frosting i just used peanut butter mixed with normal butter. Will definitely make these again!
I’m happy that they came out well! And that’s an interesting sub. I’m glad that it worked out well! Your frosting sounds delicious. :) Thanks for the tip and for your feedback!
I made this for my son today who has food allergies (I used almond milk). I absolutely loved it but he didn’t so much. I think it’s because he’s never tasted chocolate before. If I omit the cocoa powder, will the cake still come out ok? I’m thinking he may like it more of it wasn’t chocolate, but I loved how fluffy and moist this cake was so I don’t want to look for a totally different recipe.
I’m sorry for just now seeing your question! I’m happy you enjoyed them. :) Unfortunately, you can’t just omit the cocoa powder from a chocolate cake to make it a vanilla cake. It’d have to be totally reworked. Sorry about that! I wish I had a vanilla cake recipe to recommend but I’ve never found one I really love.
Has anyone tried substituting applesauce for the eggs? Or do you have a vegan gluten free cupcake recipe?
Sorry for just now seeing your question! I’ve never tried that but I do have a recipe you could use! Check out the base of these football cupcakes. They’re vegan and if you use Bob’s Red Mill 1-to-1 GF Baking Flour, they’re gluten-free, too! That’s how I make them and they’re amazing.
Hello!! Can I sub the sugar/honey with Splenda granulated sugar? Thank you!
Hi there! I’ve never used it before. Do you usually use it as a 1:1 replacement for white sugar? If so, I’m guessing it’d work here. :)
Yes it says it is a full replacement for regular sugar in recipes. Thank you. I will give it a try
I made it and loved it. Its too much “Splenda” flavor for my girls so I will play around with it and use brown sugar or something else.
That’s good to know! Thanks for coming back to let me know how it turned out. :)
How would measurements be adjusted for a double layer standard round cake?
Also for vegan chocolate frosting recipe?
You can use two nine inch round pans and bake for 30-35 minutes. I’m guessing you’d need to double the frosting but haven’t tried it and can’t say for sure.
Hey, could I add bananas to this recipe to make a banana chocolate cake? Absolutely great recipe btw, I make it all the time!
I’m happy you enjoy it! :) Unfortunately you can’t just add bananas to a recipe without adjusting a bunch of other stuff. But I do have these whole wheat chocolate banana muffins if you want to try those. :) Thanks for your comment!
Dear my grandson loves chocolate muffins. Can I replace butter for oil
Thank you ????
I haven’t tried it but I think it’d work! I hope he’ll enjoy them. :)
Hi, this recipe sounds great and I plan to try it soon. Could you please clarify-when you say mix for 2 mins, is that using a stand mixer/hand mixer or just whisk by hand? Thanks much !
Hi there! Sorry for the slow reply. Always just mix by hand unless the recipe calls for a hand mixer. :) You don’t want to overbeat the cupcakes, muffin, etc. batter! Hope you’ll enjoy the cupcakes and sorry again for the slow reply.
Used this recipe to make one round cake (halved the recipe). Absolutely delicious and by far my best chocolate cake. I reduced the sugar a tad bit and felt the sweetness was just right to eat without frosting. Thank you!
Oh my. I have no idea how I just now saw your comment! Sorry about that. I’m very happy to hear that you liked the cake and it’s great that it worked well with less sugar. :) Thanks a bunch for your feedback!
The best!
In the place where I live now, it’s very hard to get all purpose flour. The only available flour is atta flour (which I have just figured out that it is whole wheat flour). And everything I baked becoming too dense. I almost desperate in baking and I still have 5 kg of this flour!
Then I found this recipe. I made this but with 1.5 cups of sugar. My cupcakes could not stand for more than 1 day. Everyone loves it even without frosting. It’s sooo moist and light. I baked it in a cupcake shape, in a loaf shape, in a square pan, in every kind of pan available.
I will stick to this recipe.
Thank you so much! <3
I love that you bake it in every kind of pan! That’s great. :) And I’m happy you finally have something to make with your flour! This whole wheat carrot cake is also a great option. :) Thanks a bunch for your comment!
OMG!! I didnt make cupcakes, i did a regular cake in a loaf pan. just put a bit less water and used coconut oil. they are amazing! moist, loft, fluffy. We love it! It is now a go to recipe for sure. Thanks for sharing!
You’re welcome! I’m so happy you liked it! What size loaf pan did you use and how long did you bake it for? I’d love to try it out! Thanks for your feedback. :)
Just one of those we make meatloaf in, maybe 3×8 inches. it took a bit longer to cook, i dont usually keep track. if the cake is starting to smell, another 10 min it will be fully cooked.
Awesome! Thanks for the reply. :)
does one cup of honey make the cupcakes too sweet?
Nope. Otherwise I wouldn’t have called for 1 cup of honey. ;)
Just made this recipe.. looks and smells great… I can’t wait to taste it… thank you for sharing the recipe…
And thanks for your feedback! I hope you enjoyed them. :)
These came out absolutely perfect! I ran out of olive oil so I had to use 1/4 cup olive oil and 1/4 cup of grapeseed oil. I also used pure local maple syrup instead or sugar or honey. I used a little over 1/2 cup maple syrup. The batter was very thin as you said, but the finished product was perfection! This will certainly be my go-to recipe! Thank you for sharing! :)
I’m so happy that you enjoyed the cupcakes and that they worked out well with maple syrup! That’s good to know. Thanks a bunch for your comment. :)
Hi Erin! Me and the kids love this recipe. I use 3parts honey to 1 part maple syrup as the sweetener. Just wondering, do you have a banana muffins recipe similar to this?? Or any ideas how to modify this to make it banana chocolate without it being too sloppy?? Would I just add extra flour with the bananas do you think?? Thanks again for this recipe,I always have some frozen for school lunch boxes and a yummy treat when I’m craving
So happy you all like them! :) I’m in the process of moving and haven’t had internet since Sunday. I just got it on my phone but getting you the links is challenging. Just google “texanerin banana muffins” and you’ll find two options. :) Adding bananas to this recipe would require a lot of reworking. Thanks for your comment!