Paleo Coconut Cupcakes with Chocolate Frosting

By Jess

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It’s a new year, with new beginnings. Celebrate with some clean eating treats, topped with a smudge of chocolate ganache. My preferred treats to share are cupcakes. Cupcakes are easy to bake, and no one asks for a bigger or smaller slice of cake - everyone just gets one cupcake. And I have yet to try making a Paleo cake pop, so while that’s still in the works, you should try these delicious coconut flour cupcakes. And what are cupcakes without frosting? The chocolate ganache is ready in no time to top these off.

These Coconut Cupcakes will satisfy your sweet tooth without the guilt…

These Coconut Cupcakes will satisfy your sweet tooth without the guilt…

In developing Paleo recipes, I have found that my favorite recipes usually have to do with baking. I think I’ve become a baker at heart, and love to make sweet and healthy combinations to share with others. Coconut flour still baffles me though. Half a cup of flour for all of these cupcakes? Where does the substance come from? At first I thought that in order to bake Paleo recipes you needed to know some secret formula or magic trick. It turns out that neither of those is true. It’s actually very easy to use and proportion. There is also the option of using almond flour, though that uses different ratios for baking and of course isn’t nut free like coconut flour.

I also prefer simple recipes with coconut flour instead of adding in ingredients like xanthan gum or arrowroot powder. I use coconut flour instead of almond flour since almond flour is far higher in fats, and coconut flour is less expensive and one bag lasts awhile. Most importantly is the taste – the baked goods I have prepared with coconut flour have always been delicious, whether it is for bread, muffins, or pancakes. It can lend a sweeter taste to recipes but isn’t overpowering.

fresh out of the oven

When non-Paleo people like a baked recipe of mine, it’s usually a sign of a winner for me. These cupcakes are not too moist, or too dry. If you would like to cheat just a tiny little itty bit, add some sprinkles on top for added happiness.

coconut cupcake recipe


  • For the cupcakes
    • 1/2 cup coconut flour
    • 1/2 tsp baking powder
    • 1/4 tsp salt
    • 4 eggs
    • 1/3 cup maple syrup
    • 1/3 cup coconut oil, melted
    • 2 tbsp almond milk
    • 1 1/2 tsp vanilla extract
  • For the chocolate ganache
    • 4 oz. dark chocolate
    • 1/3 cup full-fat coconut milk, refrigerated


  1. Preheat the oven to 350 degrees F. Line a muffin tin with 8 cups and spray the insides with coconut oil spray to prevent sticking.
  2. Whisk together the coconut flour, baking powder, and salt in a large bowl. Add in the remaining ingredients and whisk until completely combined.
  3. Pour the batter into the muffin cups, dividing equally. Bake for 17-20 minutes, until a toothpick inserted into the center comes out clean. Place the muffin tin on a cooling rack and allow to cool for 10 minutes. Remove the cupcakes from the tin and cool completely before adding ganache.


Serving Size





Total Time

30 minutes

Prep Time

10 minutes

Cook Time

20 minutes

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Ask a Question 

  1. Thanks for sharing! These look delicious and super lofty, so rare in Paleo baked goods. I may have to try making these for my gluten- and nut-free friends.

  2. I just made these this afternoon for a Sunday treat. These are awesome! Thanks so much for posting the recipe!

  3. Thank you SO much for all the time and effort into creating so many wonderful recipes; yours seem to be the ones I choose to Pin!
    Do you find honey and maple syrup to be fairly I interchangeable or do they have their own characteristics (other than flavor)?
    Again, thank you!

    • Thanks for your comment Jane! I am so happy to be able to share recipes I love. Honey could definitely be substituted for the maple syrup in this recipe.

  4. I just want to say thank you so much for making your paleo recipes free on your website. I am new to the paleo diet and am slowly trying to change my families diet to a more healthy one. After reading many books, I am convinced that paleo is the way to go, it makes the most sense as far as diets go. I am so glad to have found your website! It helps to have recipes for all the changes I am attempting. Finding wheat free bread recipes have been a life saver, thank you!!!

  5. I made these cupcakes last night, and the family gobbled them down. I used coconut nectar instead of maple syrup. My kiddos with nut allergies loved them. Always encouraging to find peanut/almond-free Paleo goodies. The icing bowl got licked clean too! Thank you!

  6. i just made a batch tonight and my husband and i both really enjoyed them! i made the cupcakes just as your recipe has them, but the frosting was a little different, as i was using what i had on hand. i melted some “Enjoy Life” chocolate chips, added some coconut cream and then a bit of freshly ground almond butter. so good! will be making these for my non-paleo friends soon. 🙂

  7. I just made these cupcakes….yummy in my tummy!! I did add 1/2 teaspoon of almond extract (I love the way coconut and almonds taste). The texture is great and my kids love them. I made my own frosting using melted unsweetened chocolate, coconut oil, honey and cocoa powder to make it fluffy. Oh soo good. Thanks for posting!!!

  8. This came out with a dough consistency and not a batter. It could not be ‘poured’ into cups. What did I do wrong?
    The dough tastes good

  9. I was really excited to be able to make these cupcakes but I noticed that it calls for baking powder rather than baking soda.
    I currently am off all grains, sugars & starches (candida)
    Could I just substitute it with baking soda and an extra egg?

  10. Unfortunately for me I promised my coworker a cupcake… I wish I didn’t have to, but how do you store? Just covered? or refrigerated?

  11. These cupcakes are PERFECT!! Made them for my childs birthday party. Always looking for simple grain free sugar free recipes that don’t require a lot of expense…and these are awesome. I made a version with honey instead of syrup and they were great. Next time, I would allow the milk and eggs to come to room temp., as they made the honey and/or coconut oil harden in batter. Will be a fav recipe!

  12. Rebecca, thank you for your recipes, I just started paleo diet this sept 2014. I have lost 18lbs and I have enjoyed making your 14 day meal plan and all your recipes, they are tasty very good. thank you for your time and effort making my meal plan easy.

  13. I made these and my daughter and I LOVED them!! First time ever making anything gluten free, or using coconut flour. Very easy and tasty!

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