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These paleo carrot cake cupcakes are impossibly perfect. Moist, tender, and beautifully spiced – and all with no gluten, grains, refined sugar, or dairy. Great for Easter, Mother’s day, baby showers, and potlucks, this is a super easy recipe for a lighter dessert everyone can enjoy.

A paleo carrot cake cupcake topped with cream cheese frosting and chopped pecans. A bite is missing from the cupcake.

🥕 What Makes This Recipe So Good

  • These carrot cake cupcakes are moist, fluffy, perfectly spiced, and all-around unbelievably delicious. On top of that, they’re completely paleo, gluten free, grain free, refined sugar free, and dairy free. And on top of THAT – no one would ever know!! They’re so perfect that even the biggest carrot cake fans would have no idea they’re eating a lighter option.
  • It’s a super easy recipe that honestly comes together pretty quickly. It’s also basically foolproof, so even beginner bakers can totally handle this one. Plus, since it’s fairly simple, it’s a great recipe when you suddenly remember that volunteered to bring a dessert to Easter lunch, Mother’s Day brunch, a baby shower, potluck, or really any springtime event at all.
  • I may or may not be known to have eaten these for breakfast occasionally (look, they have a VEGETABLE and a FRUIT in them, ok? That counts!). If you’re wanting a breakfast option, you can skip the cream cheese frosting altogether. Without the frosting, you’ll end up with paleo carrot cake muffins moreso than cupcakes.

🧁 Cream Cheese vs. Dairy-Free Cream Cheese Frosting

If you’re paleo or avoiding all dairy, definitely go with the dairy-free cream cheese frosting option. I personally like Kite Hill and Miyoko’s the best and find them to be the closest to the real thing. The texture won’t be quite as thick as traditional cream cheese, but it’ll make the entire recipe dairy free, so that’s a big win!

If you can consume dairy, though, I recommend using regular, organic cream cheese, as it’s tangier, thicker, and richer than dairy-free cream cheese.

For anyone who typically avoids dairy but isn’t strict about it, you may want to consider using a cultured cream cheese. Like yogurt, will be easier on your digestion than conventional cream cheese. Nancy’s is a great brand to try!

👩🏼‍🍳 Chef’s Tips

  • If you don’t want thick or long pieces of grated carrot in your cupcakes, break out the food processor! After grating the carrots, toss them into the food processor bowl and pulse them ever-so-slightly until they’re very fine. Don’t overdo it, though, or you’ll end up with mushy, liquidy, puréed carrots that throw off the flavor and texture of the cupcakes. If you don’t want to deal with the food processor, you can also finely chop the grated carrots with a sharp kitchen knife.
  • If you’re not a fan of pineapple, replace the crushed pineapple with unsweetened applesauce. Like the pineapple, applesauce keeps the carrot cake cupcakes tender, moist, and still totally paleo. Feel free to use store-bought applesauce or make your own ahead of time.
  • Because of the way the flours behave and interact with the rest of the ingredients, I don’t recommend replacing the almond flour, coconut flour, or tapioca flour with any other flours. For example, coconut flour is really thirsty. If you try to replace the almond flour with more coconut flour, it’ll soak up too much of the liquid, leaving you with dry, crumbly cupcakes. Tapioca flour gives the cake that spongy texture you want – something almond flour and coconut flour can’t do.

💬 Frequently Asked Questions

Do you have to refrigerate carrot cake cupcakes?

Yes, unless you decide not to frost them! Since the frosting is cream cheese based, it needs to be refrigerated or it can spoil. Unfrosted paleo carrot cake muffins don’t contain any dairy ingredients, so they can be stored in an airtight container at room temperature.

Is carrot cake healthy?

It sounds like it should be, no? I mean, it has vegetables and fruit! Traditional carrot cakes aren’t all that healthy, though, since they’re more oil, cream cheese, refined sugar, and processed flour than they are carrots. This paleo carrot cake cupcake recipe keeps the carrots AND replaces those other ingredients with u0022healthieru0022 alternatives like coconut oil, coconut flour, almond flour, coconut sugar, and pure maple syrup.

Why did my cupcakes sink in the middle?

A couple of things could’ve caused your cupcakes to fall in the middle: Opening the oven door too early or too often. Using expired baking soda. Using too much baking soda. Over-mixing the batter. Letting the batter sit too long before baking. The oven being too hot. Filling the liners with too much batter.

Paleo carrot cake cupcakes with cream cheese frosting on a wire cooling rack.

Other Recipes You’ll Love

Recipe By: Cheryl Malik
4.99 from 64 votes

Carrot Cake Cupcakes with Cream Cheese Frosting (Paleo, Gluten Free, Dairy Free)

Prep 15 minutes
Cook 25 minutes
Cool 30 minutes
Total 1 hour 10 minutes
Packed with pineapple, pecans, spices, and carrots, like a traditional carrot cake, but gluten free, grain free, refined sugar free, and dairy free.
12 cupcakes


  • Oven
  • metal muffin pan with 12 full-size cupcake cavities
  • Cupcake liners paper or silicone
  • large mixing bowl
  • whisk
  • Silicone spatula
  • Cookie scoop with release handle optional
  • toothpicks optional, to check doneness
  • wire cooling rack
  • medium mixing bowl or stand mixer bowl
  • hand-held mixer or stand mixer
  • offset spatula or butter knife, or piping bag and piping tips


For the Carrot Cake Cupcakes

  • 2 large eggs at room temperature
  • ½ cup coconut sugar
  • cup refined coconut oil liquid, or just melted if solid
  • 2 teaspoons pure vanilla extract
  • 1 8-ounce can organic crushed pineapple drained well, approximately 1 cup; see Notes
  • 1 ½ cups grated carrots
  • 1 ½ cups fine almond flour
  • 2 tablespoons coconut flour
  • 2 tablespoons tapioca flour
  • 1 teaspoon fresh baking soda
  • 1 pinch salt
  • ½ teaspoon cinnamon
  • ¼ teaspoon ground ginger
  • ½ cup chopped pecans see Notes

For the Cream Cheese Frosting

  • 8 ounces dairy-free cream cheese softened, see Notes
  • ¼ cup pure maple syrup
  • ¼ cup refined coconut oil softened, see Notes
  • ½ teaspoon pure vanilla extract
  • 1 pinch ground ginger

Suggested Garnish (Optional)

  • finely chopped pecans


For the Carrot Cake Cupcakes

  • Preheat oven to 350º Fahrenheit. Adjust oven racks as needed so muffin pan will sit in center of oven. Line cavities of muffin pan with cupcake liners. Set pan aside.
  • Crack eggs directly into large mixing bowl. Whisk eggs vigorously until well combined. Be careful not to overmix.
  • Add coconut sugar, coconut oil, and vanilla extract to bowl. Whisk or stir well until ingredients are fully combined.
  • Add drained pineapples, grated carrots, almond flour, coconut flour, tapioca flour, baking soda, salt, cinnamon, and ground ginger to bowl. Stir until all ingredients are fully incorporated, forming thick cupcake batter. Be careful not to over-stir or batter will become dense.
    Carrot cake cupcake batter in a large mixing bowl.
  • Once batter is prepared, add ½ cup chopped pecans. Gently fold pecans into batter to distribute.
  • Use cookie scoop or spatula to portion cupcake batter evenly into cupcake liners.
    3 cupcake liners filled with carrot cake cupcake batter. A 4th, empty cupcake liner waits to be filled.
  • Place filled muffin pan in center of preheated oven. Bake cupcakes 20 minutes.
  • After 20 minutes, begin testing doneness by inserting toothpick into center of cupcakes, then immediately removing toothpick. Continue baking, checking doneness every 1 to 2 minutes, until toothpick can be removed cleanly, with few or no crumbs stuck to toothpick.
  • Once cupcakes are fully baked, carefully remove pan from oven and set aside. Let cupcakes rest in pan 5 minutes or until cool enough to handle, then transfer cupcakes from pan to wire cooling rack. Set cupcakes aside until completely cooled.
    Baked, unfrosted carrot cake cupcakes in a silver metal muffin pan.

For the Cream Cheese Frosting

  • Add softened cream cheese, maple syrup, softened coconut oil, vanilla extract, and ginger to medium mixing bowl or stand mixer bowl.
  • Use hand mixer or stand mixer to whip ingredients together until ingredients are fully combined and mixture is smooth and fluffy.
    A hand mixer beats together a cream cheese cupcake frosting until it's smooth and fluffy.
  • Use offset spatula or butter knife to dollop frosting onto center of cupcake top, then smooth dollop out to cover top of cupcake completely. Repeat until all cupcakes have been frosted. Alternately, transfer frosting to piping bag fitted with piping tip of choice, then pipe frosting directly onto cupcakes in spiral motion.
    Cream cheese frosting being spread onto the top of a carrot cake cupcake.
  • If desired, garnish top of frosting with additional chopped pecans. Serve immediately, or arrange cupcakes on tray or platter until ready to serve.
    A white woman's hand sprinkling finely chopped pecans onto the top of frosted carrot cake cupcakes.


  • Cupcake Liners: Parchment paper liners are so non-stick that they typically don’t stay on these cupcakes well. If you’re displaying these or just want them to have cute cupcake liners, I recommend using regular paper liners instead of parchment paper.
  • Coconut Oil: Unrefined coconut oil will have a stronger coconut scent and flavor. If your coconut oil is solid at room temperature, warm it just enough to melt it completely, but not so much that it’s hot.
  • Pineapple: Use organic crushed pineapple in organic pineapple juice if possible. If not, be sure your pineapple doesn’t contain any added sugar or sugar substitutes.
  • Pecans: You can omit the pecans entirely, or replace them in the batter with an equal amount of chopped walnuts or raisins.
  • Frosting: For a totally smooth, not-at-all-lumpy frosting, the coconut oil needs to be quite soft, if not melted completely. If you need to melt the oil, be sure to give it time to solidify again before trying to frost the cupcakes.
  • Cream Cheese: If you’re paleo or dairy free, use a dairy-free cream cheese like Kite Hill, Miyoko’s, or Violife. If you’re not dairy free, though, you can use traditional full-fat cream cheese instead!
  • Leftovers: Leftover cupcakes can be refrigerated in an airtight container up to 5 days. Because this recipe uses a cream cheese frosting, it’s not recommend to store the cupcakes at room temperature.

Approximate Information for One Serving

Serving Size: 1 cupcake with frostingCalories: 296calProtein: 5gFat: 22gSaturated Fat: 8gCholesterol: 48mgSodium: 189mgPotassium: 147mgTotal Carbs: 21gFiber: 3gSugar: 13gNet Carbs: 18gVitamin A: 2975IUVitamin C: 3mgCalcium: 71mgIron: 1mg
Nutrition Disclaimers
Number of total servings shown is approximate. Actual number of servings will depend on your preferred portion sizes.
Nutritional values shown are general guidelines and reflect information for 1 serving using the ingredients listed, not including any optional ingredients. Actual macros may vary slightly depending on specific brands and types of ingredients used.
To determine the weight of one serving, prepare the recipe as instructed. Weigh the finished recipe, then divide the weight of the finished recipe (not including the weight of the container the food is in) by the desired number of servings. Result will be the weight of one serving.

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  1. These did not set up but they smelled really good! They would never quite bake. I have cooked them for over 60 minutes and still mushy. Any ideas?

    1. Oh no!! That’s so odd! I’d love to troubleshoot this with you, Cate. Was your batter thick when you spooned them into the cupcake liners?

        1. Oh no! I’d love to try to troubleshoot it with you, Laura! Was the batter thick when you poured it into the cupcake liners?

  2. These were soooo good. My guests couldn’t believe they were gluten free. I substituted honey for the maple syrup. They baked perfectly and I loved that they weren’t overly sweet tasting. I did make sure the pineapple was drained super well, which I think was key.5 stars

  3. We made these last night (couldn’t find coconut sugar in time so used reg) and they were incredible. We both ate two! The cupcakes are moist (sorry) and voluminous, and the silky frosting cuts through to add a little tang. Love love.5 stars

    1. So glad you loved the cupcakes! They really are perfectly moist and delicious! Thanks for sharing, Dylan 😊 🥕

  4. No one knows it’s GF! My husband loves it when I make these. They’re soft, delicious, just the right amount of spice! I make them for bake sales for those GF folks who don’t get as many choices as others. Highly recommend!!!!!5 stars

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