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!).

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.

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! 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. :)

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.

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)

Rated 4.9 by 36 readers
100% Whole Wheat Chocolate Cupcakes (gluten-free, all-purpose options)
  • Prep Time:
  • Cook Time:
  • Ready in:
  • Yield: 24 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


  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.


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

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  • Manisha says
    May 21, 2024 @ 6:07 am

    Can I substitute oil with butter

    • Erin replies to Manisha
      May 22, 2024 @ 10:23 am

      You can, but the cupcakes wouldn’t be as moist. Butter is 80-82% fat and oil is 100%. So you’d be missing a lot of moisture!

  • Patti says
    September 13, 2022 @ 11:55 pm

    Hi Erin,

    I just wanted to let you know I made the chocolate cupcakes the ones with the boiling water. I use Bobs Rd Mill 1to 1 baking mix. I also use xylitol a cup and 1/2 aprox and one tbls of pure stevia. These things were a huge hit. They came out great. I only got 18 cupcakes. I could have gotten 20 but I filled them up almost to the top but they were still great. The xylitol’s absorbers more water so that is why I got less but still so good and fudge and my pickey neighbors had no idea they were sugar free and gluten free and vegan because I used almond milk.
    I just bought a 5lb bag of xylitol Birchwood. I even found it at Walmart. I made my ganach with it but I’m concerned that it is different in taste to the other xylitol. My ganach didn’t taste the same as the first one. I was hoping maybe you knew if they tasted different. I did forget to add a little pure stevia though. It had little cooling after taste. I used enjoy life chocolate chips and xylitol and heavy cream oh and vanilla a tsp. Taste good but I felt like I had to use more of the Birchwood. I do not have any experience with the Birchwood like I do with the regular xilitol. If you have any suggestions let me know. I also made a cheese cake with the xylitol the chocolate one from Northern nester. Came out great as well. I just wanted to let everyone know they can use the xylitol in these cupcakes and they are a little thicker but still amazing. You rock

  • Klaas
    September 23, 2020 @ 1:14 pm

    Thanks for this recipe! I subbed bananas for the eggs to make this plant-based and used 1.5 cups of sugar to offset the sugar in the bananas. Baked these in an air fryer at the same temp for 15 minutes. Still scrumptious but predictably more dense.

    • Erin replies to Klaas
      September 24, 2020 @ 8:42 am

      In an air fryer?! Whaaaat. I had no idea that this was possible! What a great idea. I love that you were able to sub bananas for the eggs. Did you weigh or measure them? How much did you use? I’d love to try that. Thanks a ton for your feedback! I’m glad that they worked well.

  • Jhanvi Matta
    September 4, 2020 @ 3:22 am

    Awesome muffins! Can we use all purpose flour and whole-wheat flour equally, instead of adding one type of flour only?

    • Erin replies to Jhanvi Matta
      September 7, 2020 @ 7:30 pm

      I’m sorry for just now seeing your question! Yes, you can mix the flour types. :)

      • Jhanvi Matta
        replies to Erin
        September 7, 2020 @ 7:32 pm

        No problem, thank you!! Loved these muffins :)

        • Erin replies to Jhanvi Matta
          September 9, 2020 @ 9:02 am

          You’re welcome! I’m glad you liked them! :)

  • HEATHER says
    September 2, 2020 @ 9:40 am

    I can’t wait to try this recipe,I love that it uses wholewheat flour. Have you added zucchini’s to the chocolate cupcakes?

  • Krista says
    February 26, 2020 @ 11:12 pm

    I make these cupcakes every year for my husband’s birthday. We love them! (Side note: I blend 400g dates with the other liquid ingredients, instead of using the sugar, for a little healthier twist.) This year my son wants to make dad a cake instead. Have you ever made these into a cake? If so, which size cake pan did you use, and any changes to cooking temp?

    • Erin replies to Krista
      April 7, 2020 @ 8:09 pm

      I’m so sorry for just now seeing your comment! It landed in spam for some weird reason. I’m so glad your husband enjoys them enough to have them every year! You can make this recipe using 2 8″ round pans. I’ve forgotten the baking time. Probably around 25 minutes but start checking at 20 to be on the safe side. I’m sorry again for the slow reply. :(

  • larry berry
    February 12, 2020 @ 1:20 am

    loved it

    • Erin replies to larry berry
      February 13, 2020 @ 12:55 pm

      Glad to hear that! Thanks for your feedback. :)


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