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. 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.

These 100% Whole Wheat Chocolate Cupcakes are so incredibly moist! They can also be made with gluten-free or all-purpose flour and are naturally dairy-free.

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.

These 100% whole wheat chocolate cupcakes are so incredibly moist! They can also be made with gluten-free or all-purpose flour and are naturally dairy-free.

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!).

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.

These 100% Whole Wheat Chocolate Cupcakes are so very moist! They can also be made with all-purpose or gluten-free flour and are naturally dairy-free.

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! Hope y’all enjoy them. :)

And if you’re in the mood for something a little more gooey, try this Hot Fudge Pudding Cake from A Family Feast. I’m pretty sure it’d be delicious with whole wheat flour!

100% Whole Wheat Chocolate Cupcakes (dairy-free with gluten-free option)

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Rated 4.9 by 25 readers
100% Whole Wheat Chocolate Cupcakes (gluten-free, all-purpose options)
  • Prep Time:
  • Cook Time:
  • Ready in:
  • Yield: 24 cupcakes

Ingredients

    Cupcakes:

  • 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!)
  • For the frosting:

  • 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

Directions

  1. Preheat your oven to 350 °F (175 °C). Line 2 muffin pans with 24 liners.
  2. In a large bowl, stir together the sugar (if using honey, don’t add it yet), flour, cocoa, baking powder, baking soda and salt.
  3. Add eggs, milk, honey (if using), olive oil and vanilla.
  4. Mix for 2 minutes on medium and then stir in the boiling water. The batter will be almost as thin as water.
  5. Fill each liner just a little more than halfway full.
  6. 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.
  7. Let cool for 5 minutes in the pans, and then turn out onto a rack to cool. Let cool completely before frosting.

Notes

  1. I’ve also used 1 1/2 cups sugar and it was still sweet enough.
  2. 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

Recipe by  | www.texanerin.com

Note: The pictures were updated in September, 2016.

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147 comments on “100% Whole Wheat Chocolate Cupcakes (gluten-free, all-purpose options)” — Add one!

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  • Prity
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    June 12, 2017 @ 3:15 pm

    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

    Reply
    • Erin replies to Prity
      June 13, 2017 @ 6:41 pm

      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.

      Reply
  • Whitney says
    May 10, 2017 @ 4:09 am

    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. 😊

    Reply
    • Erin replies to Whitney
      May 11, 2017 @ 8:00 pm

      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!

      Reply
  • Ashley
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    April 4, 2017 @ 7:46 am

    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.

    Reply
    • Erin replies to Ashley
      April 4, 2017 @ 9:12 pm

      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.

      Reply
  • Tasha
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    March 22, 2017 @ 10:13 pm

    Thank you so much for the recipe!

    Reply
    • Erin replies to Tasha
      March 23, 2017 @ 9:49 pm

      You’re so welcome! I’m happy you seemed to have liked them. :)

      Reply
  • Christa
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    February 25, 2017 @ 7:48 pm

    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!!

    Reply
    • Erin replies to Christa
      February 26, 2017 @ 9:02 pm

      I hope that they were enjoyed at the party and that your son had a great birthday! Thanks a bunch for your comment. :)

      Reply
  • Anjumara says
    February 1, 2017 @ 9:43 am

    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

    Reply
    • Erin replies to Anjumara
      February 1, 2017 @ 8:15 pm

      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!

      Reply
      • Anjumara replies to Erin
        February 13, 2017 @ 5:12 pm

        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!

        Reply
        • Erin replies to Anjumara
          February 14, 2017 @ 10:24 pm

          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.

  • Alissa
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    January 6, 2017 @ 9:17 pm

    Love love love these. Used agave nectar.
    Moist and fluffy. Amazing!!!
    ❤️❤️❤️❤️❤️

    Reply
    • Erin replies to Alissa
      January 6, 2017 @ 10:31 pm

      Aww, yay! I’m so happy that you enjoyed them! Thanks for the tip on agave and your comment. :)

      Reply
  • Litsa says
    November 19, 2016 @ 7:32 pm

    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.

    Reply
    • Erin replies to Litsa
      November 19, 2016 @ 9:20 pm

      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!

      Reply
      • Litsa replies to Erin
        November 21, 2016 @ 3:12 am

        Thank you so much. I will let you know how it turns out.

        Reply
  • Candice
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    November 14, 2016 @ 3:49 am

    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!!!!!!

    Reply
    • Erin replies to Candice
      November 14, 2016 @ 10:23 am

      Yum! Chopped walnuts sounds like a great addition. :) I’m thrilled that you liked them so much! Thanks a bunch for your comment. :)

      Reply
  • Michelle says
    October 21, 2016 @ 7:41 am

    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.

    Reply
    • Erin replies to Michelle
      October 21, 2016 @ 9:27 pm

      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. :)

      Reply
  • Celeste | The Whole Serving says
    September 21, 2016 @ 6:55 pm

    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.

    Reply
    • Erin replies to Celeste | The Whole Serving
      September 22, 2016 @ 8:15 pm

      I think you do, too. ;) I hope you’ll enjoy them! They should definitely satisfy your sweets craving. Thanks for your comment!

      Reply
  • sheryl manzano says
    September 21, 2016 @ 11:13 am

    hi :-) can I use natural unsweetened cocoa/hershey’s cocoa powder for this recipe? thank u

    Reply
    • Erin replies to sheryl manzano
      September 21, 2016 @ 3:17 pm

      Sure! That’ll work fine. I just prefer the darker kind. Enjoy! :)

      Reply
  • Laura says
    September 16, 2016 @ 4:37 am

    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!

    Reply
    • Erin replies to Laura
      September 16, 2016 @ 8:24 pm

      Thanks! I bet little ones would like my paleo cupcakes, too. ;) But it’s hard to compete with wheat!

      Reply
  • Charlotte Moore
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    September 16, 2016 @ 1:40 am

    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.

    Reply
    • Erin replies to Charlotte Moore
      September 16, 2016 @ 8:21 pm

      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. :)

      Reply
  • Melanie says
    August 31, 2016 @ 11:04 pm

    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!

    Reply
    • Erin replies to Melanie
      September 1, 2016 @ 8:21 pm

      Wow, they lasted a long time. :) That’s great. And I’m happy they were enjoyed at the BBQ! Thanks for your comment.

      Reply
  • Beena
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    August 30, 2016 @ 6:48 pm

    The best chocolate cake I have ever baked. Moist, rich, and full of goodness.

    Reply
    • Erin replies to Beena
      August 30, 2016 @ 8:45 pm

      Yay! I’m so happy you liked it. Thanks for your comment!

      Reply
  • eli
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    August 25, 2016 @ 9:03 pm

    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!

    Reply
    • Erin replies to eli
      August 26, 2016 @ 5:03 pm

      Woohoo! I’m so happy that you liked them. :) Thanks for your comment!

      Reply
  • SANGEETHA says
    July 16, 2016 @ 11:33 am

    Amazing texture and totally loved it..thanks for a recipe.

    Reply
    • Erin replies to SANGEETHA
      July 16, 2016 @ 9:39 pm

      Awesome! I’m happy they came out well. Thanks for your feedback!

      Reply
  • Casey says
    July 8, 2016 @ 2:15 am

    I dont have cocoa powder, can I sub it with dark chocolate bars in anyway? Thanks…

    Reply
    • Erin replies to Casey
      July 8, 2016 @ 7:47 pm

      That unfortunately won’t work. You really need cocoa powder for this recipe! Sorry about that.

      Reply
  • brindha says
    June 4, 2016 @ 9:00 pm

    Hi Erin, out of curiosity,,,will the eggs not get scrambled in boiling water?

    Reply
    • Erin replies to brindha
      June 4, 2016 @ 9:10 pm

      They won’t! Promise. :)

      Reply
  • Yany says
    May 21, 2016 @ 2:55 am

    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!

    Reply
    • Erin replies to Yany
      May 25, 2016 @ 8:15 pm

      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!

      Reply
      • Yany
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        replies to Erin
        June 4, 2016 @ 12:55 am

        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! :)

        Reply
        • Erin replies to Yany
          June 4, 2016 @ 6:54 pm

          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! :)

  • lauren
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    April 29, 2016 @ 3:21 pm

    This is my favorite chocolate cupcake recipe!! Could it be made it into a cake?

    Reply
    • Erin replies to lauren
      April 29, 2016 @ 9:26 pm

      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? :)

      Reply
      • lauren
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        replies to Erin
        April 29, 2016 @ 11:30 pm

        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!

        Reply
        • Erin replies to lauren
          May 1, 2016 @ 8:23 pm

          I hope you had a great birthday! And thanks for sharing the baking time for a 9×13. :)

  • Shayne Greening says
    April 26, 2016 @ 9:13 am

    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.

    Reply
    • Erin replies to Shayne Greening
      April 26, 2016 @ 8:43 pm

      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!

      Reply
  • Emily
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    April 24, 2016 @ 9:27 pm

    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.

    Reply
    • Erin replies to Emily
      April 25, 2016 @ 8:19 pm

      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. :)

      Reply
  • Casey says
    March 26, 2016 @ 11:33 pm

    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!

    Reply
    • Erin replies to Casey
      March 27, 2016 @ 7:24 pm

      I’m so happy you enjoyed them! You can never go wrong with chocolate frosting on cupcakes. ;) Thanks for your feedback!

      Reply
  • J says
    March 25, 2016 @ 10:57 pm

    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.

    Reply
    • Erin replies to J
      March 26, 2016 @ 7:43 pm

      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.

      Reply
  • Rhonda
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    March 18, 2016 @ 3:57 pm

    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!

    Reply
    • Rhonda replies to Rhonda
      March 18, 2016 @ 4:00 pm

      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.

      Reply
      • Erin replies to Rhonda
        March 18, 2016 @ 8:55 pm

        I don’t like the powdered sugar, either. :( But I’m with you – I like these even without the icing!

        Reply
    • Erin replies to Rhonda
      March 18, 2016 @ 8:54 pm

      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.

      Reply
  • Kerri
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    March 18, 2016 @ 1:14 am

    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 :-)

    Reply
    • Erin replies to Kerri
      March 18, 2016 @ 8:49 pm

      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!

      Reply
  • Meera
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    March 10, 2016 @ 12:54 pm

    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.

    Reply
    • Erin replies to Meera
      March 11, 2016 @ 9:42 am

      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!

      Reply
  • Ruchi says
    January 18, 2016 @ 3:54 am

    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 ?

    Reply
    • Erin replies to Ruchi
      January 18, 2016 @ 10:31 pm

      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. :)

      Reply

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