Gluten Free Coconut Cupcakes Recipe

Gluten Free Coconut Cupcake Recipe

I don’t mean to brag but ‘round these parts I am pretty famous for my gluten-free coconut cupcakes. People beg me for them on their birthdays, my daughter-in-law requested hundreds for her wedding reception and they have come in pretty handy when a bribe to my husband is needed. I even had a friend tell me she would gladly wait in line and pay $5.00 for just one of those cupcakes. Yep, they are well loved by the gluten intolerant and the gluten eaters alike. And with 2 cups of refined sugar, a pound and a half of butter and a pound of cream cheese in one batch, what’s not to love?

While that recipe will remain a family treasure to be brought out for special occasions, I figured it was time for a new kind of coconut cupcake – a healthier, leaner, more wholesome cupcake.

These new coconut cupcakes are not only gluten-free but grain-free, refined sugar free and dairy free as well. They contain coconut flour, coconut oil and raw agave. Coconut flour is high in protein and fiber and has fewer digestible carbohydrates than any other flour. Since coconut flour absorbs more liquid than other flours, agave is the perfect sweetener for these cupcakes. Agave is an un-refined sweetener and ranks very low on the glycemic index meaning it won’t spike your blood sugar.

My traditional cream cheese frosting has been replaced with a vegan version using Wholesome Sweeteners Organic Powdered sugar which makes it grain-free also. About a year ago Wholesome Sweeteners switched from using corn starch in their powdered sugar to using tapioca starch. If corn or grain is an issue for you, make sure you read the label to ensure you are getting the new version which is corn free. Aside from no corn, the powdered sugar has a much mellower flavor, not as sharply sweet as conventional powdered sugar.

Hmmm, all in all these cupcakes sound down right saintly to me! But shhhh, don’t tell my husband. He loves the new cupcakes and I guess I must have forgotten to mention to him that they were a healthier, leaner, more wholesome cupcake. For now, let’s just let him think of them as indulgent treats because I am pretty sure I am going to need to do some bribing again fairly soon.

5 from 1 vote
Gluten Free Coconut Cupcakes Recipe
Print Recipe

Gluten Free Coconut Cupcake Recipe

Prep Time15 mins
Cook Time20 mins
Chill time10 mins
Total Time35 mins
Course: Dessert
Cuisine: American
Servings: 12 cupcakes
Calories: 544kcal
Author: Gluten Free & More



  • ¾ cup coconut flour
  • ½ teaspoon kosher or fine sea salt
  • ½ teaspoon baking soda
  • ½ cup coconut oil
  • ¾ cup Organic Blue Agave
  • 5 large eggs – at room temperature
  • 1 teaspoon pure vanilla extract
  • ½ teaspoon pure almond extract
  • ¼ cup coconut milk
  • 1 cup coconut flakes


  • ½ cup coconut oil
  • 2 teaspoons pure vanilla extract
  • ½ teaspoon pure almond extract
  • 1 pound Organic Powdered sugar
  • 4-6 tablespoons coconut milk
  • cups unsweetened coconut chips or flaked coconut



  • Preheat oven to 350 degrees. Line 12 standard muffin cups with paper liners.
  • In a small mixing bowl, whisk together the coconut flour, salt, and baking soda until the coconut flour is no longer lumpy.
  • In the bowl of an electric mixer, preferably fitted with a whisk attachment, beat the coconut oil and agave for 2 minutes. Add the eggs, one at a time, beating well after each addition. Add the extracts and beat well to combine. Add half of the flour mixture, then the coconut milk and finally the rest of the flour mixture. Beat until combined and not lumpy. With a spatula scrape the bottom and sides of the mixing bowl to ensure all the ingredients are properly combined. Fold in the coconut flakes. Divide the mixture between the prepared muffin cups and bake for 20 -25 minutes or until the cupcakes are golden brown and a toothpick inserted into the center comes out clean. Let cool in the pan for 10 minutes then remove to a wire rack to finish cooling. While the cupcakes are cooling, make the frosting.


  • In the bowl of an electric mixer, preferably fitted with a whisk attachment, beat the coconut oil with the extracts to combine. Add the powdered sugar, 1 cup at a time and blend after each addition. The mixture may look clumpy, this is ok. Add the coconut milk, 1 tablespoon at a time until the frosting reaches desired consistency – you want it similar to butter cream frosting. Continue to beat for 2 minutes.
  • Frost the cupcakes generously and top with the coconut chips or flakes. It is best to keep the cupcakes in the fridge if not serving immediately but take them out about 10 minutes before serving to take the chill off for best results.


Nutrition Facts
Gluten Free Coconut Cupcake Recipe
Amount Per Serving
Calories 544 Calories from Fat 306
% Daily Value*
Fat 34g52%
Saturated Fat 29g145%
Cholesterol 68mg23%
Sodium 51mg2%
Potassium 142mg4%
Carbohydrates 57g19%
Fiber 5g20%
Sugar 48g53%
Protein 4g8%
Vitamin A 100IU2%
Vitamin C 0.2mg0%
Calcium 17mg2%
Iron 1.4mg8%
* Percent Daily Values are based on a 2000 calorie diet.

The views and opinions expressed on this blog are purely the blog owner’s. This blog accepts free manufacturers’ samples and forms of cash advertising, sponsorship, paid insertions or other forms of compensation. Affiliate links may be included in this post.

Disclaimer: All nutrition facts on Gluten Free & More are meant only as a guide and may differ depending on product brands used or ingredient substitutions. Some errors may occur, so you are encouraged to confirm the recipe’s ingredient and nutrition suitability for your own diet.
Have you tried this recipe? Give it a star rating and let us know your thoughts in the Ratings & Reviews section below.
Tags: Agave Coconut Cupcakes
    January 13, 2011

    Beautiful! I have a coconut cake recipe I've been meaning to modify for a while now. Your mods are a great reference.

  2. Jeanine
    January 13, 2011

    Beautiful, Carol! Although the other recipe sounds amazing, these ones you can eat without thinking how many minutes you need to add on the elliptical just for eating them. ;)

  3. The Gluten-free 'Dish'
    January 13, 2011

    Oh, these look lovely!! I want one!

  4. atxglutenfree
    January 13, 2011

    Yummy! I'm so curious to try them. I've had plenty of coconut cupcakes but not grain free! Looks delicious Carol. Thank you!

  5. Trish
    January 13, 2011

    I am in healthy cupcake heaven right now!

  6. Leanne @healthfulpursuit
    January 13, 2011

    Oh my goodness! These look fantastic! I bet you could use coconut butter as a frosting mixed with agave… hmm I'm willing to experiment!I've been having such a tough time working with coconut flour lately! Great to see it CAN work!

  7. Lisa (bakebikeblog)
    January 13, 2011

    Another winner! I have printed this off to make sometime soon! Do you think it would also work if I made it into one big cake rather than cupcakes?

  8. Jas.
    January 13, 2011

    Love it – this is the same for my gluten free vanilla cupcakes – loved by all and the recipe closely guarded! These look mighty delish – definitely going to try them!

  9. Iris
    January 13, 2011

    Guarding the family recipe, huh? Probably a good idea… I'm sure your healthier version is equally tasty though!

  10. gfe--gluten free easily
    January 13, 2011

    Coconut, coconut, and more coconut! My kind of cupcakes, Carol. :-) Thank you for this heavenly recipe!xo,Shirley

  11. Lorraine @ Not Quite Nigella
    January 14, 2011

    hehe we won't tell him that they're healthier! ;) They sound gorgeous and like real crowd pleasers! :D

  12. Simply...Gluten-free
    January 14, 2011

    Haha Ladies – no I am not keeping the original recipe a secret, it is in my dessert cookbook which will be out mid-April. So I guess I am keeping it a secret 'til then :)Leanne – that frosting sounds great, let me know! And coconut flour can be tricky but yes, it does work!Lisa – I think it will work as a cake but I would turn the temp down by 25 degrees and cook it a little slower as the coconut flour really holds on to moisture and you would want to make sure the middle gets cooked.

  13. Ellen
    January 14, 2011

    Haven't tried coconut flour yet, but these cupcakes are the recipe to try out my wings on!

  14. Jeri
    January 22, 2011

    These look delicious. Is the one cup of coconut flakes in the cupcake sweetened coconut?

    1. January 28, 2011

      Hi Jeri,

      You can use either – my family is made up of people with major sweet tooths so I used sweetened but to keep it really wholesome you can use unsweetened. Only a slight difference in sweetness factor.

  15. January 30, 2011

    They sound amazing Carol – coconut truly is a wonder food! I love that they’re so white too – I bet the sponge cake is really white inside?

    I’d just like to point up that whilst Agave syrup registers low on the glycaemic index, it is not the panacea that many believe it to be. Agave is a highly processed product that is very high in fructose. The reason it doesn’t cause your blood sugar to spike is because it’s processed in the liver rather than the gut. Fructose without the natural brake of fruit enzymes or honey enzymes, can cause blood triglycerides to rise – leading to heart disease. What you gain on one hand with blood sugar, you lose on the other with raised triglycerides!

    How about using coconut nectar or palm sugar here? These are still both high in fructose, but less processed than agave and therefore less likely to raise triglycerides.

    x x x

    1. January 30, 2011

      Hello Naomi!

      The main reason I like agave in this recipe is that coconut flour absorbs so much liquid in baking and the agave gives back some moisture. (And I love the taste!) I have a whole slew of other sweeteners I will be playing around with in the near future so we shall see…


  16. February 4, 2011

    Oh my gosh! I think these gluten free coconut cupcakes are soooo yummy! I can’t wait to try out the recipe. Thank you very much for sharing! :)

  17. February 6, 2011

    Oh my yummy, these look delish! My oldest daughter is always looking for GF treats she can make for me for Birthdays, Mother’s Day, etc. and since I’m a coconut “nut” I will have to pass this recipe on to her asap!

  18. Sheila
    February 13, 2011

    I made the cupcakes today and they baked beautifully!

  19. Matt
    March 15, 2011

    I have read few of the blog posts on your site since yesterday, and I truly like your style of blogging. I bookmarked it to my favorites internet site list and will be checking back soon.

  20. Brenda Gutierrez
    May 14, 2011

    Loved your recipe from the book!!! At first I thought they were the same recipe? Everyone loved them, including myself!

    1. May 15, 2011

      Hi Brenda – no this recipe is not the same, that one has LOTS of butter and sugar and cream cheese. Thank you so much!

  21. Tami
    July 26, 2011

    this is the one i will try first!

  22. Cristine
    August 30, 2011

    The blog was completely fantastic! Heaps of great information in this post, each of which we all need!

  23. Mandi thompson
    October 4, 2011

    I have a question??? Is it canned coconut milk?

  24. Mandi thompson
    October 5, 2011

    Ok so I figured out that it was canned milk. I made these last night for my family… And needless to say they were fabulous!! My boys asked if we could have these everyday. Thank you again,for sharing.:)

    1. October 6, 2011

      Thanks Mandi – I was traveling and I didn’t see you comment fast enough :) Glad you figured it out and enjoyed the cupcakes!

  25. Paula
    November 12, 2011

    My hubby said that these are the closest in taste to gluten cupcakes I had ever made! Really tasty

    1. November 12, 2011

      Thanks Paula! Yay!

  26. Kimberly
    December 3, 2011

    I am very excited to try this! Since I don’t bake much, would i have to double the recipe for layer cake, or would the dynamic change completely?

    1. December 4, 2011

      I think it would be totally fine – you will have to bake it longer, I am not sure exactly how much longer but check the center of each layer with a toothpick – when it comes out clean and the cake feels firm it should be done. Make sure to let cool in the pans for bit.

  27. cynthia
    December 3, 2011

    question…..can i sub fresh creamed coconut for the flakes? just made a fresh batch.

    1. December 4, 2011

      i am not sure – I am not certain what creamed coconut is but I think it should be ok.

      1. cynthia
        December 4, 2011

        It’s fresh coconut that I cream in the vitamix..coconut meat and coconut water, that’s it! But I did make the cupcakes today and decided to stick with the flake coconut…….Yum! great recipie, very moist….my first time baking with coconut flour…..great stuff:)

        1. December 5, 2011

          Aha -well I am glad you liked the recipe :)

  28. December 13, 2011

    Thank you for this great recipe! I loved it so much (and have been looking for a recipe like this for ages as my favorite cupcake is a gluten free coconut concoction) I put it on our fb wall. Thanks, again!

  29. Shiri
    January 7, 2012

    Just finished baking these and they came out delicious! My picky 5 and 3 yr olds devoured them. First coconut flour baked good that came out successful for me :)

    1. January 7, 2012

      Thanks for letting me know and YAY!

  30. Shiri
    January 7, 2012

    Also substituted the cocunut flakes for walnuts b/c my boys don’t like the texture of flaked coconut it was really good!

    1. January 7, 2012

      That sounds great!

  31. Michel
    January 13, 2012

    Great post!

  32. Amie
    January 29, 2012

    I have switched my daughter to gluten free since her last birthday and have been looking for a yummy cupcake recipe. I think I’m going to go for these.

    1. January 30, 2012

      Enjoy Amie, I hope she likes them.

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  34. Newtoglutenfree
    December 3, 2013

    Can you sub the coconut oil for canola and can you sub the agave for caster sugar?

    1. CarolKicinski
      December 8, 2013

      I think those substitutions would work just fine! Enjoy!

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  36. Jennifer
    September 25, 2014

    Hi there,
    by any chance is the butter and cream cheese coconut cupcake recipe in the “Simply Gluten Free: Cupcakes” book as well? or is it just in the “Simply Gluten-free: Desserts” book?

    1. Gluten Free & More
      September 25, 2014

      Hi Jennifer,
      There is a Coconut Cupcake recipe in the Cupcakes cookbook and it’s the same as the recipe in the Desserts cookbook. The one on my blog is a little different.

  37. Rebecca
    March 9, 2015

    I just made your cupcakes. They are very good, but I don’t use agave, and substituted honey. The honey flavor is a little strong. If I substituted regular granulated sugar, would I need to add a liquid? I’m going to make these as a gluten-free, dairy-free option for a wedding reception. I know they’ll be a hit.

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