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

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 an Easter dessert that’s a little more unique than these paleo carrot cupcakes? Try these blueberry carrot cake bars with granola from Cotter Crunch! They’re gluten-free and dairy-free and look amazing.

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 49 readers
Healthier Carrot Cake Cupcakes (paleo option, grain-free, gluten-free)
  • 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.

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

  • Erica says
    April 28, 2017 @ 4:51 pm

    These are SOOOOOO good. Thank you thank you for developing a healthy version of carrot cake. They’re simple to make and even kid approved!

    • Erin replies to Erica
      April 28, 2017 @ 6:46 pm

      Aww, yay! So happy that you and your kid enjoyed the muffins. Thanks for your comment!

  • Jacinta
    April 28, 2017 @ 6:00 am

    this is the first reciepe i have made from your website.. Definately going to try more!! Love using almond and coconut flours and these turned out perfectly! Instead of piping the frosting i spread it and topped with some chopped walnuts :-)
    Thankyou for sharing your talents 😘

    • Erin replies to Jacinta
      April 28, 2017 @ 6:48 pm

      What a nice comment! Thanks so much. I’m glad that you liked the muffins and that you’ll try out more of my recipes! I hope you’ll enjoy them just as much. Thanks again! :)

  • Angela says
    April 25, 2017 @ 12:39 am

    Do you have the nutrition info available for these muffins? They look great! Trying to monitor sugar intake

    • Erin replies to Angela
      April 25, 2017 @ 1:27 pm

      I don’t have that info but you can copy and paste the recipe here for the nutritional profile, if you’d like. :)

  • Sari Stevenson
    April 16, 2017 @ 11:53 pm

    These are outstanding. I’ve recently gone gluten free and was excited to try these. I did tweak the recipe a bit, by adding crushed pineapple and raisins, and a bit more almond flour. They turned out great.

    • Erin replies to Sari Stevenson
      April 18, 2017 @ 9:38 pm

      Yum! I’ll have to try these with pineapple and raisins. That sounds great. Thanks a bunch for your comment!

  • SF mom says
    April 16, 2017 @ 6:30 pm

    Amazing! Delicate crumble. Didn’t have coconut flour so substituted 4 tablespoons of oat flour and 2 tablespoons all purpose because it’s what I had on hand. Ran out of honey halfway into pouring it out so used a tiny bit of maple syrup to top it off. They were incredible. Just a light bit of sweetness that was perfect. This recipe is a keeper. We are not gluten-free but wanted to try something different. Thank you!

    • Erin replies to SF mom
      April 16, 2017 @ 10:12 pm

      I’m so happy that you enjoyed them! And how awesome that you decided to try them out, despite not being GF. :) Thanks a bunch for your comment! I hope you’re having a nice Easter.

  • Maria says
    April 15, 2017 @ 8:22 pm

    I just made these and they turned out WONDERFULLY!!! Since we aren’t eating them until tomorrow, would you recommend storing them in airtight containers in the fridge or is it ok to leave them in airtight containers on the counter?

    • Erin replies to Maria
      April 15, 2017 @ 8:40 pm

      I’m so happy that they came out well! An airtight container on the counter for a day or two is totally fine. Hope you have a nice holiday! Thanks for your comment. :)

  • Ann says
    April 11, 2017 @ 1:43 am

    Looks Delilah. Can this be made with egg substitute? Thanks.

    • Erin replies to Ann
      April 11, 2017 @ 8:17 am

      I haven’t tried it so I’m not sure. Sorry about that!

  • Beth says
    March 24, 2017 @ 2:17 pm

    UPDATE: I calculated 20 mini muffins to be around 6 carbs each. (I substituted maple syrup for honey). I consider this a keto friendly recipe for sure and I’m making more TONIGHT. Thanks again for sharing this lovely recipe.

    • Erin replies to Beth
      March 24, 2017 @ 9:54 pm

      That’s great! Thanks for sharing your calculations. I’m happy that they fit your diet and that you enjoy them! :)

  • Beth
    March 18, 2017 @ 2:31 pm

    I found this recipe while looking for keto or low carb desserts. I haven’t actually calculated the carb count yet but just eyeballing the recipe tells me that these are lower in carbs than standard cupcakes.
    I made 20 mini muffins and they were DELIGHTFUL. I substituted olive oil for coconut oil and maple syrup for honey. So yummy and my 4 year old ate them. The icing was perfect for me without any milk but I would like to know how everyone got their icing smooth without tiny cream cheese lumps??? Thanks for the recipe! I’ll definitely be back for more!!!

    • Erin replies to Beth
      March 18, 2017 @ 9:54 pm

      They’re definitely lower carb than regular cupcakes but not the lowest carb due to the honey. Low-carb is not my forte. ;) I’m happy that you and your little one enjoyed them! I just used a sturdy silicone spatula to make the frosting but if yours came out lumpy, try using a hand mixer. It definitely shouldn’t be lumpy! Thanks for your comment. :)

    • Jillian
      replies to Beth
      April 4, 2017 @ 8:27 pm

      Just got a tip today regarding the tiny lumps in the cream cheese.(:
      You need to whisk well the cream cheese before adding the other ingredients.


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