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Gluten Free Carrot Cake Cupcakes

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A small batch recipe for Gluten Free Carrot Cake Cupcakes with Cream Cheese Frosting made with an almond flour blend, maple syrup (refined sugar free!), and lots with sweet grated carrots.  This is an easy cupcake recipe perfect for Spring, Easter, or any occasion!

Top view of cream cheese frosted carrot cake gluten free cupcakes

Gluten Free Carrot Cake Cupcakes

Easter is approaching and that means it is Carrot Cake time!  Gluten Free, Small Batch, and Refined Sugar Free Carrot Cake Cupcakes to be exact.  And lets not forget carrot cake cupcakes that are super moist, loaded with grated carrots, and topped with a luxuriously creamy cream cheese frosting.

You may be thinking – that’s a lot of adjectives – how about you just tell me how the cupcakes taste?!  Ok, fine.  The delicious features of these cupcakes are:

  • Incredibly Moist – Applesauce is the moist-maker in these cupcakes.  And it helps with the soft and light texture.
  • Spiced to Perfection – Carrot cake requires a few spices like cinnamon, ginger, and nutmeg.  Feel free to add any more spices you prefer!
  • Sweet, Earthy Carrot Flavor – Yes, you can taste the carrots in these cupcakes.  Plus, they add the right amount of moisture to keep the cupcakes soft.
  • Topped with the expected Cream Cheese Frosting – There is a whole lot more on the frosting below – keep reading!
  • Decorated with Toasted Pecans – Because sometimes you don’t want nuts in the cake, but you still want the flavor and bite!

Key Ingredients in Gluten Free Carrot Cake Cupcakes

  1. Almond Flour, Arrowroot Flour, Coconut Flour, and Tapioca Flour – This is my go-to gluten free flour blend.  Which also happens to be a Paleo flour blend.  
  2. Pure Maple Syrup – Make no mistake, maple syrup is still sugar.  However, it is not as processed as granulated sugar and a lower glycemic swap.
  3. Fresh Carrots – Grate your own fresh carrots instead of opting for the bag of pre-shredded carrots.  Every time I eat pre-shredded carrots, it is like the flavor and moisture have been sucked right out of them!
Bite shot of a gluten free carrot cake cupcake on a mini cupcake platter

What You Need To Make Gluten Free Carrot Cake Cupcakes


In the box below the ingredients list, I have provided a little more detail on the flours in my almond flour blend.  I recommend good quality flours and have provided (affiliate) links to the brands I use in the recipe card.

  • Almond Flour – I recommend blanched almond flour.  Which means it is ground without the almond skins, and it is much finer.
  • Arrowroot Flour – Arrowroot flour is also called arrowroot starch.
  • Coconut Flour – Coconut flour does not have a strong coconut flavor.
  • Tapioca Flour – Tapioca flour is also called tapioca starch.
  • Baking Powder and Salt
  • Ground Cinnamon, Ginger, and Nutmeg – Each of these ground spices are what gives the cupcakes the trademark spice.
  • Egg – 1 large egg is all we need for this recipe.
  • Unsweetened Applesauce – The applesauce makes the cupcakes super moist, and adds a hint of flavor.  I recommend unsweetened applesauce because we are adding our own sweetness.
  • Maple Syrup – Maple syrup is a natural sweetener – meaning it is not as processed as granulated sugar.  Therefore, using maple syrup makes these cupcakes refined sugar free!  Make sure to use pure maple syrup and not pancake syrup.
  • Coconut Oil – The coconut oil is cold pressed – with a texture similar to shortening.  It is also refined, which means it won’t have a coconut flavor.
  • Vanilla Extract – Flavor!
  • Carrot(s) – 1 large or about 2 small carrots is what you will need for the grated carrots.  I recommend using regular carrots, and not baby carrots because the small ones are too hard to grate! 

Baking Equipment

  • Cupcake/Muffin Pan
  • Cupcake Liners
  • Mixing Bowls
  • Hand Held Mixer – To make the frosting.

*Paleo/Almond Flour Blend

  • Blanched Almond Flour
    • The base in the flour blend.  Almond flour produces a light and fluffy cake-like bake.  Which makes it a great option for cakes, cupcakes, muffins, and even gluten free cookies.  I will always recommend a blanched, super-fine almond flour.  This means the flour is ground as fine as it can be (before turning into butter), and the skins are removed.
  • Arrowroot Starch/Flour
    • Flour and starch are used interchangeably in the package titles.  Arrowroot aids in the tender texture we like in baked goods.  It also adds structure to the crumb.  
  • Coconut Flour
    • Ground from dried coconut meat, coconut flour is super absorbent.  It should be blended with other flours as it does not work well as a 1:1 swap.  Its absorbency allows swapping granulated sugar for liquid sweeteners –  like maple syrup or honey.  I also find it counter-balances other wet ingredients in the recipe.
  • Tapioca Starch/Flour
    • Another where flour and starch are used interchangeably in package titles.  Tapioca adds a little more chew to the baked good – where normally we’d get that from gluten in all-purpose flour.  And I have found in baked goods, it gives a ‘crisp’ exterior.

Cream Cheese Frosting For Carrot Cake Cupcakes


  • Cream Cheese – I recommend full fat cream cheese because it makes the frosting thick and creamy.
  • Unsweetened Canned Coconut Milk – Refrigerate the can of coconut milk overnight so the coconut solids and liquid separate.  We only use the coconut solids to make the frosting.
  • Powdered Sugar – I like to use an Organic Powdered Sugar, but any powdered sugar will work.
  • Vanilla Extract – Flavor!

My recipe for cream cheese frosting is made without butter.  I like to use the coconut solids from a can of unsweetened coconut milk for a couple of reasons:

  1. It makes the frosting extra creamy
  2. While creamy, it doesn’t have a heavy taste or texture.

Frosting Ideas for Carrot Cake Cupcakes

I like to think of Carrot Cake Cupcakes as a modest, yet extremely indulgent, dessert.  Which is why I don’t get too elaborate with the frosting and decorations.  Similar to the simple frosting I did on the Mini Carrot Cake with Pineapple.  

  • You can pipe the frosting onto the cupcakes using a piping bag and tips
  • Or, you can dollop the frosting on top then smooth out with a small offset spatula.  Which is what I did with these cupcakes.

To decorate the cupcakes, because nuts seem to be a required ingredient for (most) carrot cake recipes, I opted to put toasted chopped pecans on the top.  

Tips For Making Gluten Free Carrot Cake Cupcakes

  • Use regular size, fresh carrots – No baby carrots here!  1 large or 2 small carrots is what you will need for the recipe.
  • And no pre-shredded carrots – They lack the flavor and moisture of fresh carrots.  In my opinion.
  • Grate the carrots on a box grater – To make sure you have nice size carrot pieces, I recommend grating the carrots on the large holes of a box grater.
  • Use unsweetened applesauce – Because we are adding our own sweetener to the cupcakes.  Sweetened applesauce may overpower the flavor.
  • Bring the refrigerated ingredients to room temperature – This allows the batter to mix and incorporate better if all of the ingredients start at the same temperature.
  • Use pure maple syrup – And not pancake syrup.  Pure maple syrup adds the perfect amount of sweetness without imparting an over-powering flavor.
  • Cool the cupcakes completely – For two reasons:  1.  gluten free baked goods taste better when they are completely cool, and 2.  you don’t want to frost warm cupcakes!
Platter of gluten free carrot cake cupcakes on a table

Common Questions For How To Make Gluten Free CArrot Cake Cupcakes

Can this recipe be doubled to make a larger batch of cupcakes?

I haven’t tested a larger batch, but if you do, let me know how it turns out!

Can I make this into a cake instead?

You certainly can! You can use a 6-Inch round cake pan to make a single layer cake.

Will a 1:1 gluten free flour work instead of the almond flour blend?

I’ve only tested the recipe using the almond flour blend. However, in my experience testing 1:1 gluten free flours, they don’t swap 1:1. And I find that they make the bake dry.

What does the applesauce do for the cupcakes?

Applesauce is great for making the cupcakes moist!

Can I swap a different sweetener for the maple syrup?

I haven’t tested the recipe using a granulated sugar, therefore I can’t say how they will turn out. I don’t recommend honey because it bakes differently and requires ingredients adjustments to account for its acidity.

Will baby carrots work?

You can certainly try using baby carrots, but they will be hard to grate!

My cupcakes are sticking to the cupcake liners. What can I do?

Let the cupcakes cool completely, and the liners will come off easier.

How should I store leftover cupcakes?

I recommend covering and refrigerating frosted cupcakes because of the cream cheese frosting. Otherwise, un-frosted cupcakes can be stored covered at room temperature.

Close up of gluten free carrot cake cupcakes on a cake platter

More Small Batch Easter Recipes

Carrot cake cupcake with cream cheese frosting on a mini cupcake stand

Gluten Free Carrot Cake Cupcakes

Yield: 5 Cupcakes
A small batch recipe for Gluten Free Carrot Cake Cupcakes with Cream Cheese Frosting made with an almond flour blend, maple syrup (refined sugar free!), and lots with sweet grated carrots.  This is an easy cupcake recipe perfect for Spring, Easter, or any occasion!
Prep20 minutes
Cook24 minutes
Total44 minutes


  • 1 – Muffin/Cupcake Pan


Carrot Cake Cupcakes

  • 1/4 cup, + 2 tabplespoons blanched almond flour
  • 3 tablespoons arrowroot flour
  • 1 and 1/2 tablespoons coconut flour
  • 1 and 1/2 tablespoons tapioca flour
  • 1/2 teaspoon baking powder
  • 1/8 teaspoon salt
  • 1/2 teaspoon ground cinnamon
  • 1/4 teaspoon ground ginger
  • 1/4 teaspoon ground nutmeg
  • 1 large egg (room temperature)
  • 1/4 cup unsweetened applesauce (room temperature)
  • 1/4 cup pure maple syrup
  • 2 tablespoons cold pressed refined coconut oil, melted
  • 1/2 teaspoon vanilla extract
  • 1/3 cup fresh carrots, grated (about 1 large or 2 small)

Cream Cheese Frosting

  • 4 ounces cream cheese (room temperature)
  • 1/4 cup unsweetened canned coconut milk, full fat (refrigerated overnight; only the cream in the can)
  • 1/2 cup powdered sugar
  • 1/2 teaspoon vanilla extract
  • chopped pecans or walnuts, for topping (toasting the nuts is optional, but recommended)


Carrot Cake Cupcakes

  • Preheat the oven to 350F degrees and adjust the oven rack to the middle position. Line a cupcake pan with 5 cupcake liners.
  • In a small mixing bowl, whisk together the almond flour, arrowroot flour, coconut flour, tapioca flour, baking powder, salt, and ground spices.
  • In a medium mixing bowl, add the egg, applesauce, maple syrup, oil, and vanilla extract. Whisk together until smooth. Add the carrots and stir to combine.
  • Sprinkle the dry ingredients over the wet ingredients and stir until no dry streaks remain. Equally portion the batter into the cupcake liners. Tip – Use a cookie scoop to make portioning easier! Bake the cupcakes for 22 to 24 minutes until a toothpick inserted in the middle comes out mostly clean, and the cupcakes are springy to the touch.
  • Cool the cupcakes in the pan set on a wire cooling rack for 10 minutes. Then transfer the cupcakes to the cooling rack to cool completely.

Cream Cheese Frosting

  • Refrigerate the can of coconut milk overnight. This causes the coconut liquid and solids to separate. We are only using the coconut solids. You will have leftover coconut milk – see recipe Notes below for some ways to use them.
  • In a medium mixing bowl, add the cream cheese, coconut solids, and vanilla extract. Using a hand held mixer and medium-high speed, beat until smooth and creamy. Add the powdered sugar in small increments (to avoid a mess), and beat until the frosting is fluffy and creamy. You can add more or less powdered sugar depending on your sweetness preference, and how thick you want the frosting.
  • Optional – Toast pecans or walnuts to top the cupcakes (as pictured). Sprinkle the nuts evenly onto a baking sheet and toast at 350F degrees for 5 to 7 minutes.
  • On completely cool cupcakes, pipe or spoon the frosting on the cupcakes, sprinkle with chopped nuts and Enjoy!
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Ideas For Leftover Coconut Milk
Course: Dessert
Cuisine: American
Author: Erin Cernich
Nutrition information is calculated by a third-party and should only be considered an estimate and not a guarantee.
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about the author ...

I'm Erin and I'm all about desserts - and a little bit of butter!

I've tested, written, and photographed hundreds of recipes on my website. Here you'll find the tastiest small batch gluten free and traditional desserts - all homemade, all simple, and all for you!

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