Gluten Free Carrot Cake Cupcakes with Cream Cheese Frosting

Perfectly spiced and featuring a super moist crumb, these gluten-free carrot cake cupcakes are paired with a velvety whipped cream cheese frosting, making them the ideal dessert for Easter, holidays, or any special occasion.

Why You'll Love These Gluten-Free Carrot Cake Cupcakes

The Perfect Spice Blend: A fragrant quartet of cinnamon, ginger, nutmeg, and cloves delivers that classic, deep carrot cake flavor in every bite.
Unbeatably Moist & Tender: We’ve nailed the texture—expect an incredibly soft crumb (thanks to the addition of almond flour and applesauce) and perfectly fluffy without ever feeling heavy or oily.

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

Ingredients

Gluten Free Flour Blend: A blend of almond flour and Bob's Red Mill Gluten-Free 1-to-1 Baking Flour is the secret to this tender crumb. The almond flour adds essential moisture and structure that standard gluten-free blends sometimes lack.
The "Ultimate" Spice Mix: To get that classic, deep flavor, we use a specific harmony of cinnamon, nutmeg, and ginger, finished with a pinch of cloves. This combination ensures the cupcakes aren't just sweet, but aromatic and warm.
Applesauce & Oil (The Moisture Secret): By splitting the fats between unsweetened applesauce and melted refined coconut oil, you get a moist, soft cupcake that never feels greasy. Avocado oil works great here too, but avoid olive oil—its strong flavor will compete with the spices!
Freshly Shredded Carrots: For the best results, use whole carrots that you peel and grate yourself. Avoid pre-bagged shredded carrots; they are often treated to stay dry in the bag, which will lead to a dry cupcake. After grating, give them a quick rough chop. Finer carrot pieces distribute more evenly, so you get a bit of carrot in every single bite.
Full-Fat Cream Cheese: Always use room-temperature, full-fat block cream cheese for the frosting. This ensures a velvety, thick texture and that signature tangy flavor that balances the warm spices.

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

How To Make Gluten-Free Carrot Cake Cupcakes

Step 1: Grate and Prep the Carrots. Peel and chop whole carrots into 3″ pieces. Using a KitchenAid attachment, food processor, or box grater, shred the carrots quickly.
Step 2: Chop the carrots. Once shredded, give them a final rough chop so the finer pieces distribute evenly throughout the batter.

Steps showing how to make gluten-free carrot cupcakes. Start by grating the carrots and the dicing them into small pieces.

Step 3: Whisk the Dry Ingredients. In a medium-sized bowl, whisk together the gluten-free flour, almond flour, baking powder, baking soda, salt, cinnamon, ginger, nutmeg, and cloves.
Step 4: Beat the Eggs and Sugars. In a large bowl or stand mixer fitted with the whisk attachment, beat the eggs, cane sugar, and dark brown sugar on medium-high speed for 4–5 minutes.

Whisk together the dry ingredients, and then beat together the dark brown sugar, sugar, and eggs until light and fluffy.

Step 5: Combine and Fold. Add the dry ingredients to the wet mixture, mixing until just combined. Turn off the mixer and use a spatula to gently fold in the shredded carrots (and any optional mix-ins) until they are evenly distributed.
Step 6: Divide the batter. Using a large cookie scoop, divide the batter evenly among the liners, filling them about ¾ full to prevent the batter from spilling over as they rise. Bake for 18–22 minutes.

Gluten free carrot cake cupcakes mixture, then fully baked.

Decorate with Cream Cheese Frosting

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

Cream cheese frosting on gluten free carrot cake cupcakes.

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

Ways To Shred Carrots For Carrot Cake

While the KitchenAid shredding attachment is my favorite way to grate carrots quickly, there are two other easy methods you can use:

Box Grater: After peeling, use either a box or a plane grater to shred the carrots by hand. This is a great workout and gives you full control over the texture!
Food Processor: Peel and cut the carrots into 3″ pieces. Attach the shredding blade to your food processor and "shred away" for a fast, hands-off approach.

Storage & Make-Ahead Tips

To Store: Keep leftover cupcakes in an airtight container in the refrigerator for up to 4 to 5 days.
To Freeze: For long-term storage, wrap individual unfrosted, cooled cupcakes tightly in plastic wrap and place them in a freezer-safe bag or container. They will stay fresh for up to two months. When you're ready to enjoy, thaw them at room temperature before frosting.
Make-Ahead Instructions: You can prepare and frost these cupcakes up to one day in advance. Store them covered in the refrigerator, but be sure to pull them out 20–30 minutes before serving to let the frosting soften and the flavors shine!

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

More Gluten-Free Easter Desserts

Common Questions

Can I use this recipe to make a full-sized cake?

Absolutely! You can easily convert this cupcake recipe into a traditional layered carrot cake. Here is how to do it:

Double the Recipe: To yield enough batter for a standard layer cake, simply double all the ingredients.
Prep Your Pans: Grease and line two 8-inch round cake pans with parchment paper for easy removal.
Bake: Divide the batter evenly between the prepared pans and bake at 350°F (180°C) for 25–35 minutes, or until a toothpick inserted into the center comes out clean.
Cool Properly: Let the cakes rest in their pans for 10 minutes before transferring them to a wire rack. It is vital to let them cool completely before you begin frosting to prevent the cream cheese from melting.

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.