Healthier Carrot Cake Cupcakes (grain-free, gluten-free, paleo option)

Moist, lightly sweetened with honey and even a little fluffy, these grain-free and gluten-free healthier carrot cake cupcakes (or muffins!) are the perfect Easter treat. With a paleo and dairy-free option.

First up, if you prefer a grain-containing healthier carrot cake recipe, I have you covered! This 100% whole grain carrot cake is the best carrot cake I’ve ever had. Hands down.

These naturally sweetened grain-free and gluten-free carrot cake cupcakes have the best light and fluffy texture! With a paleo and dairy-free option.

If grains aren’t your thing, these healthier carrot cake cupcakes are awesome. I feel like a broken record, just because I say this all the time, but I used a combination of almond flour and coconut flour to achieve the perfect texture. I want my grain-free baked goods to taste as close to grain-containing ones as possible and these are pretty darn close!

People often ask if there’s a substitute for coconut flour and there really isn’t. You can easily order it online or you can make your own homemade coconut flour! And the only substitute for the almond flour would be almond meal (which is a lot cheaper than almond flour!) or another nut flour.

These gluten-free and grain-free carrot cake cupcakes have the best fluffy texture! With a paleo and dairy-free option. Naturally sweetened with honey.

So now that we’ve got the healthier carrot cake cupcakes out of the way, we need some healthier cream cheese frosting! This is the same cream cheese frosting recipe that I used in my last post on carrot cake scones.

It uses just a little maple syrup as sweetener. I really thought cream cheese frosting without powdered sugar was impossible but this maple syrup version was just as good! It’s quite thick so if you want to thin it out, just add some milk.

I’m just guessing that if you’re interested in grain-free baking, you’re not into mounds of frosting on top of your cupcakes. The amount that this cream cheese frosting recipe yields is just enough for a thin slathering on each cupcake. If you want to pipe it like I did, you can pipe about twice as much as you see in the pictures.

These gluten-free and grain-free carrot cake cupcakes have the best fluffy texture! Naturally sweetened and with a paleo and dairy-free option.

I recommend frosting the cupcakes right before serving because once you frost them, they need to be refrigerated. They can sit at room temperature for about 4 hours so if you want to frost them in preparation of a party – no problem! They just taste better and fluffier if you keep them at room temperature and microwaving cream cheese frosting sounds like a bad idea.

Obviously cream cheese isn’t dairy-free but there are dairy-free cream cheeses out there. If you don’t like the thought of using that, just leave out the frosting or use my vegan cream cheese recipe.

It’s naturally sweetened, doesn’t have any unusual ingredients and is also paleo-friendly! Half the recipe should yield enough for a nice slathering on top of each cupcake. You can also find my directions for making these carrot cake cupcakes into an 8″ cake on that post.

Want more grain-free treats?!

  • These paleo chocolate banana muffins are bursting with banana flavor and are super rich and decadent! (honey sweetened, grain-free, gluten-free and dairy-free)
  • Vegan Paleo Lemon Cookies {grain-free, gluten-free, dairy-free}
  • Vegan Paleo Lemon Cookies {grain-free, gluten-free, dairy-free}
  • These paleo chocolate cupcakes are moist but not eggy and have a rich, dark chocolaty taste! (grain-free, gluten-free, and dairy-free)

Healthier Carrot Cake Cupcakes (grain-free, gluten-free, paleo and dairy-free options)

Rated 4.9 by 37 readers
Healthier Carrot Cake Cupcakes (grain-free, gluten-free, paleo option)
  • Prep Time:
  • Cook Time:
  • Ready in:
  • Yield: 8 muffins


    For the carrot muffins:

  • 1 1/4 cups (125 grams) blanched almond flour
  • 2 tablespoons (16 grams) coconut flour
  • 1/2 teaspoon baking soda
  • 1/8 teaspoon salt
  • 1 1/2 teaspoons ground cinnamon
  • 1/2 teaspoon ground ginger
  • 1/4 teaspoon ground nutmeg
  • 2 large eggs, room temperature
  • 1/3 cup (75 grams) refined coconut oil, melted (if you use unrefined coconut oil there may be some coconut taste to the muffins)
  • 1/3 cup (106 grams) honey
  • 2 teaspoons vanilla
  • 1/2 cup (50 grams) grated carrots
  • For the cream cheese frosting: (for paleo / dairy-free, use a half batch of this vegan "cream cheese" frosting)

  • 2 ounces (56 grams) cream cheese
  • 4 teaspoons maple syrup
  • 1 1/2 teaspoons vanilla
  • a dash of salt
  • additional milk for thinning, if desired


  1. Preheat the oven to 350°F (175°C). Line a muffin tin with 8 muffin liners.
  2. In a medium bowl, mix together the dry ingredients (almond flour through nutmeg). Set this aside.
  3. In a large bowl, mix together the eggs, oil, honey, and vanilla.
  4. Add the dry mix to the wet mix just until combined and then gently fold in the grated carrots.
  5. Divide the batter evenly among the liners and bake for 17-20 minutes or until a toothpick inserted in the middle comes out clean.
  6. Let the muffins cool for 5 minutes in the pan and then remove to a wire rack to cool completely. Do not frost until completely cool!
  7. For the cream cheese frosting, mix everything together until thoroughly combined. If it's too thick for your liking, add a teaspoon of milk at a time until it's your desired consistency.
  8. Spread a thin layer on top of each cupcake or pipe it on. Do note that if you pipe it, you'll have some leftover if you pipe it as lightly as I did in the pictures.

Recipe by  |

Pin post on Pinterest Share post on Facebook Share post on Twitter Share post on Google+

180 comments on “Healthier Carrot Cake Cupcakes (grain-free, gluten-free, paleo option)” — Add one!

  • Eve
    August 22, 2016 @ 3:21 pm

    Hello from over the pond in Blighty! I just had to post to say how fantastic these little beauties are! I made them yesterday and they have been unceremoniously gobbled up by my husband, daughter and myself ;-) Being gluten and dairy intolerant I have hugely missed my carrot cake and cuppa moments, but no more!!! Thanks again from a very happy (and full!) fan :-)

    • Erin replies to Eve
      August 23, 2016 @ 9:02 pm

      And hello to you from Germany! :) I’m so happy to hear that you and your family enjoyed the cupcakes and that you don’t have to miss carrot cake anymore. Thanks a bunch for your comment!

  • Robin says
    August 12, 2016 @ 7:32 pm

    These carrot cake cupcakes are quite possibly one of my most favorite sweet treats ever! I added 1/4t. salt because I like a little more salt in my baked goods and I did not make the icing. I also added raisins to some of them which tasted great! I warmed them up and ate them with grass fed butter, cinnamon and salt on them, soooooooooooo delicious!! They froze well too. Thank you for using honey as the sweetener as it’s the only one I’m supposed to use! Awesome recipe!

    • Erin replies to Robin
      August 13, 2016 @ 7:21 pm

      Aww, yay! I was so happy to read how much you liked the cupcakes. :) Added raisins sound great and it’s good to know that they freeze well! Thanks for the tips and for your feedback. :)

  • Susie
    July 19, 2016 @ 6:24 am

    My 8-year-old daughter just made these (with some help from me) for her daddy’s bday. We all loved it. We like to try different things bc my daughter doesn’t like traditional carrot cake and sweets in general. These however, weren’t overly sweet and hit the spot. Thank you so much Erin!

    • Erin replies to Susie
      July 19, 2016 @ 12:27 pm

      That’s great that your daughter (and the rest of you!) enjoyed the cupcakes. :) And I’m jealous of your daughter not really liking sweets. I wish I were the same. ;) Thanks a bunch for your comment!

  • blu says
    June 30, 2016 @ 3:22 pm

    can i use butter instead of coconut oil?

    • Erin replies to blu
      June 30, 2016 @ 4:50 pm

      I haven’t tried it but I think that’d work fine. :) Enjoy!

  • Linda says
    June 25, 2016 @ 9:13 pm

    I think doubling the amount of carrots would make more like true carrot cake, although this is very good, I increased nutmeg and added one ripe banana. I used coconut flower and regular gluten free flour. Texture was perfect.

    • Erin replies to Linda
      June 26, 2016 @ 7:18 pm

      I’m happy that they came out well, especially with all your changes! Thanks for your comment. :)

  • Veronica says
    June 10, 2016 @ 11:22 am

    Thanks for this recipe it is very easy to follow…quick to make and absolutely delicious! These are some of the best muffins I have ever made!

  • Catherine says
    May 28, 2016 @ 2:29 pm

    My son is intolerant to almonds, is there anything i can use to replace it? Thank you!

    • Erin replies to Catherine
      May 28, 2016 @ 5:47 pm

      Nut flours are usually interchangeable with other types of nut flours so you could try that. And I haven’t tried this myself but supposedly you can make your own sunflower seed flour and it works as a sub for almond flour. I hope that helps!

  • Arlete
    May 5, 2016 @ 8:23 pm

    We recently found out that our 4 year old has celiac disease and so all my family recipes are no longer easy to recreate. Thank goodness I found your recipe and it was approved by the whole family including my 4 year old picky eater :)
    I used freshly grated nutmeg and maybe next time I will put a little less and more cinnamon. I love cinnamon! Overall it was perfect, very moist. I just had another one for breakfast! I also loved using the weights. Thank you again and have a great day!

    • Erin replies to Arlete
      May 5, 2016 @ 9:56 pm

      I’m so happy that you found something that your 4 year old and the rest of the family could enjoy! And I agree that more cinnamon is never a bad thing. ;) I’ll have to try these with freshly grated nutmeg and see if that yields a stronger taste than the pre-ground stuff. Thanks a bunch for your nice comment!

  • Kristelle
    April 27, 2016 @ 8:42 am

    I rarely leave reviews because I hardly ever follow a recipe closely enough to feel like I can really comment, but I did this time, and they were great! Okay, I maybe skimped a little on the nutmeg and cinnamon, but I weighed all the main ingredients. THANK YOU for giving weights, I love to cook with a scale–so easy. Plenty sweet for my taste, and texture was nice. Just little oily, but that seems to happen with coconut oil sometimes, didn’t detract cuz we’re not afraid of a little coconut oil. :)

    • Erin replies to Kristelle
      April 28, 2016 @ 11:51 am

      I love weights, too! I wish everyone who made my recipes would use them so that the recipes would come out exactly as intended. ;) I’m so happy that you enjoyed the cupcakes! Thanks a bunch for your comment and taking the time to leave a review. :)

  • Willow
    April 21, 2016 @ 11:48 pm

    These were tasty, but didn’t quite taste like carrot cake. I thought I’d be able to taste all of the different spices, but all I could taste was the nutmeg. There was a bit too much and next time I’ll just use a little less. They were still tasty, though, and the cream cheese frosting was delicious!

    • Erin replies to Willow
      April 24, 2016 @ 8:21 pm

      Hmm. Did you use freshly grated nutmeg? I didn’t, so I wonder if that could be it. I’ve never noticed these being especially nutmeg-y. But I’m happy you still liked them! Thanks for your feedback. :)

  • Ashley says
    April 16, 2016 @ 3:13 am

    These look Awesome! Thanks for the recipes.

    • Erin replies to Ashley
      April 18, 2016 @ 12:47 pm

      Thanks, Ashley! And you’re welcome. :)

  • Melanie
    March 30, 2016 @ 8:21 am

    These are great! I made them for Easter for my niece who is GF/DF/SF, and also made a traditional carrot cake for the rest of us at the party. I was hoping there would be extras for me to take home but everyone really enjoyed these and ate them all before I could sneak any away. I’m so happy to have found a healthy alternative to traditional carrot cake!

    • Erin replies to Melanie
      March 31, 2016 @ 7:41 pm

      Aww. I’m sorry there were no leftovers! But I’m quite happy that everyone liked them so much. ;) Thanks so much for your feedback!

  • Catherine Nault says
    March 16, 2016 @ 4:36 pm

    Has anyone substitued the almond flour for something different? Or even did half almond half something else? One of my kids is sensitive to almonds and bothered by carrots during pollen season and I’m thinking those 2 ingredients together might be overload for her and induce her asthma? Any ideas????

    • Erin replies to Catherine Nault
      March 17, 2016 @ 12:02 pm

      Almond flour and other nut flours are only interchangeable with other nut flours so you could try a different nut flour / meal. But if she’s bothered by carrots, I’d suggest finding a different recipe because there’s no sub for it in these cupcakes. Sorry about that!

    • Cheryl replies to Catherine Nault
      March 25, 2016 @ 10:03 pm

      You can make a “One Minute Muffin” for your allergic daughter using coconut flour or ground flax. You can put fruit or nuts in them if you are just looking for a “cup cake” kind of dessert for this child. Look it up online, there are tons of variety out there.

      • Erin replies to Cheryl
        March 26, 2016 @ 7:44 pm

        I’d never heard of those! They look so easy. Thanks for sharing. :)

      • Catherine Nault replies to Cheryl
        March 27, 2016 @ 5:14 pm

        Cheryl, thank you for that info, I’ll definitely have a look for that recipe. :)

  • Corrin
    February 28, 2016 @ 10:11 pm

    I am making these for the second time – they are that good! I have not made frosting -just eat them as is. Delicious! Thanks for creating a healthier alternative for my carrot cake obsession:)

    • Erin replies to Corrin
      March 1, 2016 @ 9:45 pm

      And thank you for your nice comment and feedback! I’m so happy you enjoyed them. :)

  • Emma says
    February 26, 2016 @ 5:26 pm

    Hi Erin, can these be made without an electric mixer? Just by hand? Also, what type of ginger do you mean? Minced ginger like you would use in asian cooking, or is it a powdery dry ground ginger? Thanks for your help! Emma

    • Erin replies to Emma
      February 26, 2016 @ 5:37 pm

      Hi Emma! No electric mixer is needed. :) Just mix everything together by hand. And you’ll want to use ground ginger. I hope you’ll enjoy them!

      • Emma replies to Erin
        February 26, 2016 @ 6:51 pm

        Thanks Erin!

  • Ann says
    February 25, 2016 @ 9:42 pm

    can these be made without eggs? like with phylum husks?

    • Erin replies to Ann
      February 25, 2016 @ 10:33 pm

      I’m sorry but I haven’t tried an egg-free version! I know one person used flax eggs but since I haven’t tried it, I can’t guarantee it’d work. I hope they’ll come out well if you give it a try. :)

  • Pam
    February 19, 2016 @ 4:04 am

    I added nuts and raisins and they came out kind of heavy. Do I need to change the recipe?

    • Erin replies to Pam
      February 19, 2016 @ 7:55 pm

      They’re light and kind of fluffy without the nuts and raisins so I’m guessing they did weigh them down (though I’ve never had that problem in other recipes!) I wouldn’t recommend changing that recipe because you’re not actually adding or changing anything to the make-up of the batter. Perhaps you could just use less? Sorry I don’t have a better answer for you!

  • jennifer says
    December 29, 2015 @ 2:29 am

    Do you know if these freeze well? or how long they stay fresh? or… what the best way to store them is?

    Thanks! :)

    • Erin replies to jennifer
      December 29, 2015 @ 2:37 am

      They stay fresh for 2-3 days at room temperature (without the frosting) and I haven’t tried freezing them but I imagine they’d be fine. And to answer your other question, I’m not sure about subbing maple syrup for honey. A lot of people do that but maple syrup is so much thinner and less sticky than honey so I never recommend it unless I’ve tried it myself. I hope your kid has a great birthday. :)

  • jennifer says
    December 28, 2015 @ 6:14 pm

    Hi! I’m thinking about making these for my 1 year old’s bday party. Do you think I can sub maple syrup for the honey?

    • Erin replies to jennifer
      January 15, 2016 @ 9:58 am

      Oh, no! I remember typing out a reply but I’m not seeing it here for whatever reason. I’m so, so sorry! I said that maple syrup is more runny and less sticky than honey so I’m not quite sure if it’d work out well. Did you try it out? Sorry again! :(

  • Kate says
    October 22, 2015 @ 10:30 pm

    These look amazing! Could I use olive oil instead of coconut oil and almond flour instead of coconut flour, do you think? Thanks

    • Erin replies to Kate
      October 22, 2015 @ 11:02 pm

      Thanks! :) Olive oil should work but coconut flour can’t really be subbed. It absorbs a lot more liquid than every other flour and so there aren’t really any subs for it. Sorry about that!

  • pam holton says
    September 23, 2015 @ 4:50 am

    Have you tried these with just coconut flour? I made your vanilla cupcakes and they were perfect! Thanks much.

    • Erin replies to pam holton
      September 23, 2015 @ 3:04 pm

      I’m so happy you liked the cupcakes! Do you mean the coconut flour based ones in the Samoa cupcake recipe? And I haven’t tried these with coconut flour, unfortunately. Coconut flour isn’t really interchangeable with any other flours so I’m afraid it wouldn’t work. Sorry about that!

  • Olga
    August 19, 2015 @ 6:59 am

    Can I sub stevia for the honey? How much? Do I need to add something else for moisture then?

    • Erin replies to Olga
      August 19, 2015 @ 11:00 am

      I unfortunately don’t have any experience with Stevia so I have no idea how much you’d need or how much liquid to add. Sorry about that!

  • Stephanie says
    June 30, 2015 @ 12:05 am

    These came out perfect! Thank you so much for this recipe! :)

    • Erin replies to Stephanie
      July 13, 2015 @ 10:13 pm

      I’m so happy that they came out well and so sorry for not seeing this comment until now! Thanks for the feedback. :)

  • Margaux
    June 6, 2015 @ 11:40 pm

    Amazing! My mom and I are major food freaks, trying to lay off the junk food, and these were just perfect! Definitely making again!

    • Erin replies to Margaux
      June 7, 2015 @ 8:14 pm

      I’m so happy that you both enjoyed them! Good lucking with the healthy eating and thanks so much for your feedback. :)

  • Michele says
    April 30, 2015 @ 3:21 pm

    I made these up for my dad who is diabetic. He love carrot cake but hasn’t eaten it for years. He ate them as a dessert and for breakfast. He was so happy when his blood sugar levels were in normal range after having these. Thank you so much for this recipe, you have made an old man very happy! And his daughter.

    • Erin replies to Michele
      May 10, 2015 @ 11:25 am

      How awesome that your dad could eat these without having any blood sugar issues. :) He must be so happy that he can have carrot cake again! Thanks a bunch for your nice comment and feedback and so sorry for my super slow reply.

  • Stephanie
    April 21, 2015 @ 6:05 pm

    I made this for a women’s meeting at church this morning. I swapped out the honey for xylitol. I made the “frosting” with swerve (to taste) and almond milk. They turned out really good. Thank you for sharing.

    • Erin replies to Stephanie
      April 23, 2015 @ 10:06 pm

      I’m so happy that they were enjoyed by all! And good to know that xylitol works. Thanks for the feedback and for the tip! :)

  • Melissa Carr
    April 7, 2015 @ 5:03 am

    I tried these tonight and they were fabulous! I used 2/3 cup honey & added 3-4Tbsp of almond milk to it and it was perfect! I used my almond meal pulp from the almond milk I make. It tends to be a bit dryer than the blanched almond meal. I have to use it in SOMETHING since we make so much almond milk around here:) They were moist and cake like! I put on some vanilla frosting(coconut milk/powdered sugar/vanilla) and it was the best:) High fiber too! Thanks for such a great recipe!

    • Erin replies to Melissa Carr
      April 7, 2015 @ 3:32 pm

      I’m so happy that you enjoyed them! Your changes sound great and I love that you were able to use your leftover almond pulp. :) So much better than just throwing it away! Thanks so much for your feedback. :)

  • Teressa says
    April 1, 2015 @ 9:17 am

    Any idea on nutrition info? Specifically carbs, sugar and fiber grams?? Looks amazing trying to find low carb naturally sweetened muffins/cupcakes.

    • Erin replies to Teressa
      April 2, 2015 @ 5:52 pm

      You can copy and paste the ingredients here for that info. I hope that helps! :)

  • Sara
    March 31, 2015 @ 3:15 am

    What is the cooking time difference if I make a round cake instead of cupcakes?

    • Erin replies to Sara
      March 31, 2015 @ 9:13 pm

      Check out this post (first paragraph after the second picture) for more info but basically, double the recipe and bake it in 2 8″ pans for 17 minutes. Your cake will be super thin if you don’t double it (there are pictures in that post, too!) I hope that helps and that you’ll enjoy it. :)

  • Fred says
    March 10, 2015 @ 7:56 pm

    For some reason mine didn’t turn out at all. The batter was not really like batter. I had to add about 1/4 cup water and it still just when into muffin cups like a lump. I followed the recipe exactly even weighed it. I used an almond flour I made myself from left over meal I had from almond milk I made. I ground it finer and sifted it and it looked fine. Maybe will try buying the flour next time to compare.

    • Erin replies to Fred
      March 10, 2015 @ 8:09 pm

      I’m pretty sure the problem was the homemade almond flour (although it still shouldn’t have been lumpy!) Did you dehydrate the almond pulp? If you didn’t, that could explain it. I made these again last week and don’t recall the batter being thick at all. I’m sorry that they didn’t work out! I hope your next version with store bought almond flour will come out better. :)

      • Fred replies to Erin
        March 10, 2015 @ 9:39 pm

        I will try Bob’s brand and see. Gauging moisture content is a guessing game for me but if it grinds fine I figure I must be in the ballpark. I thought about that factor as well. I’ll let you know how my next batch turns out. Can’t rate recipe yet but the comment response time is awesome. Thanks.

        • Erin replies to Fred
          March 10, 2015 @ 9:49 pm

          No problem! And I’ve used Bob’s Red Mill in these without issue so I’m confident your next batch will turn out better. :)

  • Astaaria
    March 9, 2015 @ 12:56 pm

    These are amazing, I made 24 mini muffins and baked for 10 minutes, worked out perfectly. The kids love them with a bit of cream cheese spread on top.

    • Erin replies to Astaaria
      March 10, 2015 @ 7:59 pm

      I’m so happy that they came out well and that you and your kinds enjoyed them! I bet they were cute as mini muffins. :) Thanks a bunch for your feedback!


Comments? I’d love to hear from you!

Your email address will not be published. Required fields are marked with *


Comments are moderated. If you don’t see your comment immediately, don’t panic… it went through! Thank you so much for taking time to leave feedback!

Please help others by rating the recipe: