Paleo Chocolate Cupcakes

After the vanilla cupcakes were all gone, I was feeling empty inside. Well, not totally empty—just a little snackish. You know when you want something sweet but not anything really healthy. And since I still had my bag of coconut flour, I thought why not try some chocolate cupcakes?

These are just as good as the vanilla ones if you ask me. They do have a stronger taste of coconut, but I think it helps since the cocoa powder needs a fatty flavor to give it some chocolaty richness.

Paleo Chocolate Cupcakes

Prep time: 10 minutes

Cook time: 35 minutes

Ingredients(Makes a dozen cupcakes):

  • 1/2 cup +2 Tablespoons coconut flour
  • 4 eggs
  • 2 egg whites
  • 1/3 cup cocoa powder
  • 1/2 cup cane or palm sugar
  • 1 cup coconut milk
  • 1/2 teaspoon baking soda
  • 1 teaspoon vanilla extract


  1. Preheat your oven to 350 degrees and line 12 cupcake holders with paper liners.
  2. Mix together the coconut flour, eggs, egg whites, cocoa powder, sugar, coconut milk, baking soda, and vanilla extract in a large bowl.
  3. Slowly add just enough water so that the batter is slightly runny and easy to mix by hand without exerting too much effort.
  4. Scoop the batter evenly into the cupcake liners. Hit the pan against the counter a few times to even the batter and knock out any air bubbles.
  5. Bake for 30-35 minutes until the tops are firm to the touch.

If you like these cupcakes, you might like my paleo vanilla cupcake recipe.

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55 Responses to Paleo Chocolate Cupcakes
  1. Faith @ For the Health of It
    January 27, 2012 | 10:05 am

    Those look delish! I know full Paleo isn’t right for me, but I am really interested in trying out some of their grain-free options. I’m headed to WF tonight – maybe I can score some coconut (or almond) flour there to play with this weekend!

  2. christina
    January 27, 2012 | 10:44 am

    Chocolate Ganache already sounds fancy when you say it aloud, but then you stick the word Paleo in front of it?? I just want to say it all day and pretend I’m sophisticated…which we know is far from the truth.

  3. Caroline @ chocolate & carrots
    January 27, 2012 | 10:47 am

    I’m loving these! 😀

  4. Gina @ Running to the Kitchen
    January 27, 2012 | 10:50 am

    Coconut milk just got added to the grocery list. I could think a million things that ganache would be delicious on top of!

  5. Kim
    January 27, 2012 | 12:54 pm

    YUM!! These look really good!

  6. Amber K
    January 27, 2012 | 2:59 pm

    Yum! These look delicious.

  7. Brandon @ Kitchen Konfidence
    January 27, 2012 | 5:53 pm

    Looks delicious 🙂 Do they taste of coconut at all?

    • Wannabe Chef
      January 27, 2012 | 7:07 pm

      These definitely taste more coconutty than the vanilla cupcakes I made, but it works well because the cocoa powder has no richness on its own.

  8. Hannah
    January 28, 2012 | 2:28 am

    I don’t know if I can hold out until the first Monday of next month when my health store has a 20% off sale and the coconut flour becomes not quite as expensive…

  9. Anna
    January 28, 2012 | 4:23 am

    It is still a beauty even with the choco ganache on top. There is beauty in messy chocolate that only the taste buds can see…A must try!

  10. C&C Cakery
    February 8, 2012 | 1:31 am

    Loved your vanilla paleo cakes (as did my paleo friends). I know I’m gonna love these! Thanks so much for experimenting with this way of eating. I love seeing what create 🙂

  11. Britta
    February 24, 2012 | 3:45 pm

    I am having my version in the oven now – they look GREAT! Cant wait for m kids to come home from school to try them wih me:-)
    Thank you for sharing great paleo recipes!

  12. Julia
    March 12, 2012 | 6:45 pm

    Since I’ve been eating a more paleo-ish diet, I’ve been loving experimenting with paleo ‘sweets’ This looks SUPER good!!!

  13. cassidy
    April 24, 2012 | 4:31 pm

    can you use honey or agave instead of sugar? if so how much should i substitute?

    • Wannabe Chef
      April 24, 2012 | 4:35 pm

      Yes, you can use 1/2 cup of liquid sweetener. In that case I’d reduce the coconut milk by about 2-3 Tablespoons.

  14. […] owe these treats today to the ever-inventive Evan, as I adapted them from the lime variant of his many coconut cupcake creations. Thanks […]

  15. […] paleo chocolate cupcakes get their depth not from coconut flour but coconut milk. Even without oil or melted chocolate, they […]

  16. rebecca
    August 5, 2012 | 4:45 pm

    How can these be paleo if they have sugar in them?

    • Wannabe Chef
      August 5, 2012 | 6:09 pm

      They aren’t 100% paleo but dessert isn’t really a part of the paleo diet, either. If you used palm sugar, it’d be considered closer to the diet.

    • Emma
      August 15, 2012 | 1:09 pm

      It’s cane sugar, so it’s healthier than regular sugar.

  17. Angie
    October 18, 2012 | 8:04 pm

    Are you using coconut milk in the can or regular drinking coconut milk from a carton?

    • Wannabe Chef
      October 18, 2012 | 8:07 pm

      I use canned

      • Angie
        October 18, 2012 | 8:20 pm


  18. Christy
    June 4, 2013 | 1:54 pm

    I made a batch of 6 chocolate cupcakes on Friday which turned out great, and were absolutely delicious! I had one on Sunday as well, and they still tasted yummy! I have an event this Saturday and wanted to know how many days prior to the event that I can make the cupcakes and them still taste fresh?! I don’t have much time on Saturday to bake them! 🙁 would Thursday be too long?

    • Wannabe Chef
      June 4, 2013 | 1:58 pm

      I would try to make them Friday if you could but if you keep them extra cold and then let them sit at room temperature Thursday should be fine.

  19. Kristen Zimmerman
    July 14, 2013 | 8:18 pm

    Do they freeze well? Need some for kids to take to school as their alternative. Thx!

    • Wannabe Chef
      July 14, 2013 | 8:42 pm

      I haven’t tried to freeze this recipe but I imagine that they would.

  20. Joyce
    October 7, 2013 | 11:56 am

    I would like to use whole eggs instead of all whites- but not sure how many whole eggs to use? Any suggestions?

  21. Joyce
    October 7, 2013 | 11:59 am

    Oops, re-read the recipe more carefully… 4 eggs plus 2 whites! Whew… some days are skiddy-whompus, today is one of them!

    • Wannabe Chef
      October 7, 2013 | 12:05 pm

      Haha, those days are called Monday mornings for me, too.

  22. Jessica
    October 8, 2013 | 1:40 pm

    Hi, I want to make these for my son’s first birthday this week, with honey I think. Can you share what you topped the cupcakes with? Thanks!

  23. […] Ingredients: 1/2 cup +2 Tablespoons coconut flour 4 eggs 2 egg whites 1/3 cup natural unsweetened cocoa powder(NOT Dutched) 1/2 cup coconut palm sugar ( I used evaporated cane juice) 1 cup coconut milk (I used regular ol’ raw cows milk cause I didn’t want too much coconut flavor) 1/2 teaspoon baking soda 1 teaspoon vanilla extract Instructions: Preheat your oven to 350 degrees and line 12 cupcake holders with foil liners. (Be sure to use foil liners. I used paper ones, and there was a lot of sticking, which wasn’t so nice. Update: they don’t stick quite so much if you let them cool completely first.Lesson learned.) Or if you are making them mini, it makes around 30. Mix together the coconut flour, eggs, egg whites, cocoa powder, sugar,  milk, baking soda, and vanilla extract in a large bowl. If your batter isn’t “runny” add just a tad of water. Scoop the batter evenly into the cupcake liners. Drop the pan lightly onto the counter to smooth the batter and knock out any air bubbles.(I did this and mine still had some air bubbles. Apparently I didn’t bang enough. So, really bang it, just don’t let the batter fly out!) Bake for 30-35 minutes for regular, and 15-20 minutes for mini – until the tops are firm to the touch. Lightly adapted from The Wannabe Chef […]

    December 4, 2013 | 1:05 am

    I was wondering, does the recipe still work if I use zero calorie sugar instead of palm sugar, or do I need to make more alterations?

    • Wannabe Chef
      December 6, 2013 | 11:28 am

      If the zero calorie sugar you use is granular and advertises a 1:1 substitution with regular sugar then it should be fine.

  25. Andie
    January 13, 2014 | 11:28 pm

    Can I substitute almond flour for coconut flour?

    • Wannabe Chef
      January 13, 2014 | 11:31 pm

      Almond flour doesn’t quite bake like coconut flour so it’s not suitable for a 1:1 substitution. I’d recommend looking for a cupcake recipe designed to use almond flour.

  26. Andie
    January 14, 2014 | 12:25 am

    Got it. Thanks!

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  29. melodee
    April 13, 2014 | 1:49 pm

    Can I use almond flour/meal? I am not able to find coconut flour well I found it but it was sold out

    • Wannabe Chef
      April 13, 2014 | 7:33 pm

      This particular recipe won’t work with almond meal. However if you look under the cakes/frosting section of my recipes there should be one or two almond-based cake recipes there that might suit you.

  30. Andrea Prow
    June 23, 2014 | 2:09 am

    Could you use xylitol instead of the cane or palm sugar??

    • Wannabe Chef
      June 23, 2014 | 9:08 pm

      I haven’t tried it so I can’t say for sure but I think it would work!

  31. Actsingdance4Christ
    July 2, 2014 | 5:21 pm

    Did you use full-fat coconut milk, or can I use lite (about 50 calories per 1/3 cup)?

    • Wannabe Chef
      July 3, 2014 | 9:25 pm

      This recipe works best with full-fat but you can use a lighter version; the cake will just be less moist..

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    July 17, 2014 | 6:24 pm

    […] 47. Paleo Chocolate Cupcakes Recipe […]

  33. Becky
    October 8, 2014 | 1:12 am

    Do you have the recipe for the chocolate frosting in the picture?

  34. DIY Recipes! | Smart Start Susie
    October 18, 2014 | 10:59 am

    […] Paleo Chocolate Cupcakes (made a cake instead) – I’ve been looking for a clean eating cake recipe for my son’s birthday next month. I would use this recipe again, might try it with whole wheat flour and add some more sugar. Coconut flour and Almond flour have a distinct texture and I’m not sure I’m a fan of using either for a cake. […]

  35. Dani
    October 25, 2014 | 10:56 pm

    Do you know how this would do in a cake pan vs. cupcakes? My birthday is next week and I’m looking for a recipe that will work as an actual round without sinking. Just curious! Thanks so much!

  36. Danielle Guerrero
    April 30, 2015 | 12:47 am

    I was wondering how many carbs and sugars were in the coc and the vanilla paleo cupcakes? my daughter has type 1 diabetes and I’m thinking about making these for her bday. thank you!

  37. tina
    July 2, 2015 | 7:29 am

    these sound delicious but can i use honey instead of the cane sugar? and how much would i need ?

    • Wannabe Chef
      September 20, 2015 | 3:36 pm

      You can try using 1/2 cup honey in place of the sugar, and add a couple of minutes to the baking time to account for the extra moisture. The cupcakes will probably come out a little more dense that way