Gluten-Free Carrot Cake Cupcakes

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These gluten-free carrot cake cupcakes are perfectly spiced with a super moist crumb, paired with a velvety whipped cream cheese frosting. Perfect for special occasions and holidays.

Gluten-Free carrot cake cupcakes with cream cheese frosting, topped with babys breath.

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Why You Will Love This Gluten-Free Carrot Cake Cupcake Recipe
Gluten-Free Carrot Cake Cupcake Ingredients
Ingredient Notes
How To Make Gluten-Free Carrot Cake Cupcakes
Make Cream Cheese Frosting & Decorate
Ways To Shred Carrots
Substitutions & Variations
Storage
Tips For Success
More Gluten-Free Desserts You'll Love
FAQ
Recipe
Reviews

Why You Will Love This Gluten-Free Carrot Cake Cupcake Recipe

These gluten-free carrot cake cupcakes are the perfect dessert for Easter or any special occasion. Here are some reasons why you will love this recipe:

Perfectly spiced. When it comes to carrot cake, it's all about the spice. The combination of cinnamon, ginger, nutmeg, and cloves gives these cupcakes the most incredible flavor.
Moist cupcakes with a tender crumb. The texture of these cupcakes is both soft and fluffy, without being overly oily.
Easy to make. These gluten-free cupcakes are super easy to make with simple ingredients.

Gluten-Free carrot cake cupcakes with the wrapper peeled away exposing the moist and tender carrot cake.

Gluten-Free Carrot Cake Cupcake Ingredients

You will need the following ingredients to make these delicious carrot cake cupcakes:

Ingredient shot for gluten-free carrot cake cupcakes.

For the cream cheese frosting, you'll need:

Ingredient shot for cream cheese frosting.

Ingredient Notes

Gluten-Free Flour + Almond Flour: A combination of gluten-free and almond flour helps create a tender crumb. My favorite gluten-free flour blend to use is Bob's Red Mill Gluten-Free 1 to 1 Baking Flour.
Baking Powder + Baking Soda: Both leavening agents help lift the cake.
Spices: Ground cinnamon, nutmeg, ginger, and a pinch of cloves are the ultimate carrot cake spice mix.
Sugar + Dark Brown Sugar: Using dark brown sugar adds moisture to the cupcakes, while regular cane sugar helps sweeten.
Apple Sauce + Oil: Using a mix of oil and unsweetened applesauce gives you a soft, moist texture without the cake feeling greasy. I prefer to use melted refined coconut oil which is a healthier option compared to vegetable oil. You could also use avocado oil but olive oil is not recommended due to its strong flavor.
Eggs: Two large eggs at room temperature.
Vanilla Extract: Organic high-quality pure vanilla extract gives both the cupcakes and frosting a touch of sweetness.
Freshly Shredded Carrots: You will want to use whole fresh carrots that are chopped, peeled, and grated. Don’t use pre-bagged shredded carrots as these lack moisture and will create dry cupcakes. Use a box grater, food processor, or stand mixer attachment to shred the carrots. After you’ve finished shredding, give the carrots a rough chop, so the pieces are even finer and can be distributed evenly in each cupcake.
Cream Cheese: Room temperature is key, and using full-fat cream cheese is recommended. Its thick texture and tangy flavor pair perfectly with the carrot cupcake's warm spices.
Butter: Softened unsalted butter adds stability and richness to the frosting. You can also use ghee. For best results, sifting the powdered sugar first with a fine mesh sieve can help eliminate any extra lumps in the frosting.
Powdered Sugar: I’m using organic powdered sugar to help create that classic sweet, and fluffy cream cheese frosting.

Find the printable recipe card with full instructions and measurements below.

How To Make Gluten-Free Carrot Cake Cupcakes

Steps showing how to make gluten-free carrot cupcakes. Start by grating the carrots and the dicing them into small pieces. Whisk together the dry ingredients, and then beat together the dark brown sugar, sugar, and eggs until light and fluffy.

Preheat the oven to 350°F. Line a 12-cup muffin tin with cupcake liners.

Grate the carrots. Peel and chop the whole carrots into 3″ long pieces. Weigh the carrots on a food scale to ensure you have the right amount. (The final weight should be 200 grams, but keep in mind some of the carrots will get stuck in the blade while grating, so you'll want to add closer to 220 grams.) Attach the KitchenAid shredding attachment and grate the carrots quickly. You can also shred the carrots in a food processor or grater.
Finely chop the carrots. After you’ve finished shredding, give the carrots a rough chop, so the pieces are finer and can be distributed evenly into each cupcake. Weigh the carrots once again to make sure you have 200 grams.
Whisk the dry ingredients. In a medium-sized bowl, whisk together the gluten-free flour, almond flour, baking soda, salt, cinnamon, nutmeg, ginger, and ground cloves.
Combine the wet ingredients. Using a large bowl or stand mixer with a whisk attachment beat eggs, sugar, and dark brown sugar on medium-high speed, for 4-5 minutes. The mixture should be doubled in volume, light and fluffy. (This helps to create an aerated, light crumb). Slowly pour in the melted oil, apple sauce, and vanilla extract. Mix for another 1-2 minutes, until combined.

Add the dry ingredients into the wet ingredients of the carrot cake cupcakes, then fold in the shredded carrots. Pour the batter evenly into the cupcakes liners and bake.

Add dry ingredients to wet the ingredients. Mix until just combined with a few floury streaks remaining and then turn off the mixer.
Fold in the grated carrots. Using a spatula, fold in the shredded carrots and any mix-ins until evenly blended throughout the batter.
Divide the batter. Using a large cookie scoop, pour the batter evenly into the liners, filling only about ¾ full to avoid spilling over the sides.
Bake and cool the cupcakes. Bake for 18–22 minutes, (our cupcakes are fully baked at 20 minutes) or until a toothpick inserted in the center comes out clean. Transfer the cupcakes to a wire rack and allow them to cool completely before frosting.

Make Cream Cheese Frosting & Decorate

Make the cream cheese frosting by combining softened cream cheese and powder. Add the powdered sugar, salt, and vanilla extract, and beat until light and fluffy. Frosted and cooled cupcakes photo.

Make the cream cheese frosting. Add the softened butter and cream cheese to a large mixing bowl or stand mixer with a paddle or whisk attachment. Beat together on high speed until smooth and creamy. Scrape down the sides of the bowl. Add the powdered sugar, vanilla extract, and salt. Beat on low speed for 30 seconds and then switch to high speed and beat for 1-2 minutes or until light fluffy and fully combined.
Decorate the cupcakes. Using a piping bag with a 1M piping tip, decorate the cooled cupcakes and top with optional garnish if desired.

A bite taken out of a gluten-free carrot cake cupcake.

Ways To Shred Carrots

While I’m using my KitchenAid shredding attachment to grate the carrots quickly, there are two other ways to shred carrots.

Grater: Peel the carrots and use either a box or plane grater to grate the carrots.
Food Processor: Peel and cut the carrots into 3″ long pieces. Attach the shredding blade to your food processor and shred away.

Substitutions & Variations

There are many variations and substitutions to make these gluten-free carrot cupcakes to fit your needs.

Adjust the spices: Instead of ground cloves, you can use ¼ teaspoon of cardamom or ¼ teaspoon of allspice.
Add mix-ins: Use a ½ cup of your favorite mix-ins including chopped walnuts (our favorite) chopped pecans, raisins, or coconut flakes.
Make brown butter cream cheese frosting: For a frosting with added depth of flavor, make a brown butter cream cheese frosting. Here is a step-by-step post on how to brown butter. Once the butter is browned, transfer the melted butter to a bowl and place the bowl into the refrigerator to re-solidify. Then allow it to soften to room temperature and proceed to make the recipe as directed.
Dairy-Free: The carrot cake cupcakes are both gluten-free and dairy-free. To make gluten-free dairy-free frosting, use dairy-free cream cheese and dairy-free butter.
Nut-Free: Replace the almond flour with an equal amount of gluten-free 1 to 1 baking flour.

Storage

To store: Leftover carrot cake cupcakes should be stored in an airtight container and covered, in the fridge for 4 to 5 days.
To freeze: Wrap the individual cooled unfrosted cupcakes tightly with plastic wrap then place the cupcakes in a freezer-safe container or ziplock bag. Freeze for up to two months and thaw at room temperature. Frost fully thawed cupcakes and enjoy!
Make ahead instructions: Cooled and frosted cupcakes can be made ahead 1 day in advance, covered, and stored at room temperature or in the refrigerator. Just make sure to pull them out of the refrigerator 20-30 minutes before serving.

Tips For Success

Here are a few tips for the best gluten-free carrot cake cupcakes.

Freshly grate and chop your carrots. Don’t use pre-shredded carrots as they’re quite dry and lack the moisture needed for this recipe. Freshly shred or grate approximately 1 and ½ cups (200g) of moist carrot shreds. Before measuring on a food scale, give the shreds a rough chop so the pieces are finer and distributed nicely in each cupcake.
Weigh all of your ingredients. I can't emphasize this enough. It is super important to weigh all of your ingredients on a food scale to get accurate results.
Use a cookie scoop to divide the batter. The easiest way to fill the cupcake liners is to use a large cookie scoop. It helps to evenly distribute the batter without making a mess.
Line your cupcake pan. To prevent the cupcakes from sticking to the pan, make sure to use cupcake liners. If you find that the liners stick to the fully baked cupcakes, I have a really easy hack. Melt a small amount of refined coconut oil in a bowl. Using a silicone pastry brush, gently tap the end of the brush in the oil and ever-so-lightly, brush the inside of the cupcake liner. You want to use the smallest amount of oil to just dot the liners, otherwise the cupcakes will become too greasy. Then pour in the cupcake batter.
Let the cupcakes completely cool before frosting. Cooling the cupcakes completely before frosting will prevent the frosting from melting.
Frost the cupcakes and decorate using your preferred method. If you do not have a pipping bag or piping tips, you can use an offset spatula to decorate your cupcakes. Add a few chopped walnuts or pecans to the top of the frosting if desired.

Gluten-free carrot cake cupcakes exposing the soft tender middle.

More Gluten-Free Desserts You'll Love

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FAQ

Do gluten-free carrot cake cupcakes need to be refrigerated?

The frosted Carrot Cake Cupcakes can be left at room temperature for several hours, but you will want to store any leftovers exceeding 8 hours in the refrigerator.

Can I use this cupcake recipe to make a gluten-free carrot cake recipe?

Yes, you can double this recipe to make a traditional carrot cake instead of cupcakes. Grease and line two 8-inch round cake pans with parchment paper. Divide the batter into the greased cake pans and bake for 25-35 minutes, or until a toothpick inserted into the center of the cake comes out clean. Remove the cakes from the oven and let them cool in the pans for 10 minutes. Then transfer the cakes to a wire rack to cool completely before frosting.

Can I use butter instead of oil in this recipe?

Butter is not recommended as it will yield a dryer cake. The combination of oil and apple sauce keeps these cupcakes perfectly moist without being too oily or too dry.

How do you know when the cupcakes are finished baking?

Insert a toothpick into the center of a cupcake. If the toothpick comes out clean, the cupcakes are done baking.

Can I divide this recipe in half to make a small batch recipe?

Yes, this recipe divided in half will make 6 carrot cake cupcakes.

I hope you love these Gluten-Free Carrot Cake Cupcakes as much as I do! If you make it, I’d love to hear how it turned out in the comment box below. Your review will help other readers in the community.