These wheat free dark chocolate cupcakes are the among the best healthy chocolate cupcake recipes I have made. Instead of the typically overconsumed and often allergenic wheat flour, they are made with nutritious spelt flour.


Spelt flour does contain gluten, so these are not gluten-free (you can find a gluten-free chocolate cake recipe here).

I usually use raw chocolate powder in my dark chocolate recipes, but I ran out…I used Rapunzel brand organic cocoa powder instead, along with organic sugar and just a little organic butter. I was really pleased with how super “chocolate-y” and absolutely scrumptious these turned out.

As far as chocolate dessert recipes go, I think these are pretty healthy, and they will make a great addition to your healthy chocolate recipes collection. Just know that for optimal health, all sugar, even organic sugar, should be limited as much as possible, and it should be avoided if you are trying to lose weight.

If you really like dark chocolate, you could try reducing the sugar by 1/4-1/2 cup.

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  1. 1

    Rose — May 25, 2009 @ 7:46 pm

    made the crazy delicious organic chocolate cupcakes … so delicious and widely appreciated. also, maybe the easiest recipe ever.

    used yogurt instead and they felt pretty dense when i first took them out, but they stayed really moist.

    i have to ‘fess up to making a chocolate butter frosting as i lamely didn’t have creme fraiche or agave … but really it was childhood flashback i needed. next time, i’ll be fully organic …

  2. 2

    Michelle — May 26, 2009 @ 7:20 pm

    I love that it uses sea salt. I just love the flavor of it, in virtually all that I cook!

    I get mine @

    I’m eager to try this recipe!!

  3. 3

    drwinnie — May 30, 2009 @ 4:51 am

    I am so glad the cupcakes worked out with yogurt!
    And I think everyone needs a little “real” frosting now and then…not at all lame!

  4. 4

    Terry — July 1, 2009 @ 4:54 pm

    Any suggestions on how to adjust recipe to exclude the eggs? I am very excited to have found your website!!

  5. 5

    drwinnie — July 1, 2009 @ 7:30 pm


    You can mix 1 Tb. ground flax seeds with 3 Tb. water as a substitute for each egg in baking; so in this recipe you would use 2 Tb. ground flax and 6 Tb. water instead of the eggs, and allow to sit for a few minutes before mixing with the other ingredients. Let me know how that works out…

  6. 6

    Tera — March 13, 2011 @ 1:27 pm

    Wow….so decadent. I used 1 cup of sugar vs 1.5 cups. They still turned out fantastic. I may try to lower the sugar a bit more next time. I substituted 2/3 cup almond milk and 1/3 cup vanilla yogurt for the buttermilk and it worked out fabulous. This is a keeper!

  7. 7

    MamaPutu — June 10, 2013 @ 12:08 am

    Made these for my hard-to-please family and they were a hit. I added shaved coconut and cocoa nibs to the cupcakes, and I used a raw mint/cashew/agave/coconut oil icing. Yum!

  8. 8

    Muskaan — February 26, 2014 @ 2:15 pm

    wow! would love to try this but I had a question. Is 1/4tsp of baking soda enough for the whole recipe? Most of the muffin recipes ask for at least 1tsp of baking soda or baking powder.

    Can I reduce cocoa powder by 1/2 and increase the spelt flour by 1/2 cup?

    Thanks for sharing such a yummy recipe.