Carrot Cake Cupcakes (Gluten-Free) with Cream Cheese Frosting

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.

Course Dessert

Cuisine American

Diet Gluten Free

Prep Time 25

Cook Time 20

Cooling and Frosting Time 1 30

Total Time 2 15

Servings people

Calories 443kcal

Author Rebecca Taig

Ingredients

Carrot Cake Cupcakes

Dry Ingredients

1 cup + 2 Tablespoons (153g) gluten-free flour, Bob's Red Mill Gluten-Free 1 to 1 Baking Flour
¼ cup (25g) almond flour
1 teaspoon baking powder
½ teaspoon baking soda
½ teaspoon salt
2 teaspoons cinnamon
1 teaspoon ground ginger
½ teaspoon nutmeg
⅛ teaspoon cloves

Wet Ingredients

2 large eggs, at room temperature
¾ cup (150g) dark brown sugar
¼ cup (50g) sugar
¼ cup (60g) unsweetened applesauce
¼ cup (60g) refined coconut oil, melted and slightly cooled
1 teaspoon vanilla extract
1½ cups (200g) peeled, shredded, and coarsely chopped carrots (about 3-4 large carrots)

Cream Cheese Frosting

8 ounces (224g) full-fat block cream cheese softened to room temperature
½ cup (113g) unsalted butter, softened to room temperature
3 cups (360g) powdered sugar, sifted
1 teaspoon vanilla extract
⅛ teaspoon salt

Instructions

Make Carrot Cake Cupcakes

Prepare the Muffin Pan. Preheat the oven to 350°F. Line a 12-cup muffin pan with cupcake liners.
Grate the Carrots. Peel and chop whole carrots into 3″ pieces, then weigh out approximately 220g. (You’ll want that extra 20g to account for what gets stuck in the shredder!) Using a KitchenAid attachment, food processor, or box grater, shred the carrots quickly.
Finely Chop the Carrots. Once shredded, give them a final rough chop so the finer pieces distribute evenly throughout the batter. Weigh one last time to ensure you have exactly 200g of moist, fresh carrots.
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. Set this aside.
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. You are looking for the mixture to double in volume and become light and fluffy—this aeration is the secret to a light, tender crumb! Once achieved, slowly pour in the melted coconut oil, applesauce, and vanilla extract, mixing for another 1–2 minutes until fully combined.
Combine and Fold. Add the dry ingredients to the wet mixture, mixing until just combined; it's okay to still see a few floury streaks. 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.
Portion and Bake. 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—ours are usually perfect at the 20-minute mark—or until a toothpick inserted into the center comes out clean.
Cool Completely. Transfer the cupcakes to a wire rack and allow them to cool completely. This is a crucial step to ensure your frosting stays perfectly whipped and doesn't melt!

Frost Cupcakes

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.
Decorate the Cupcakes. Using a piping bag with a 1M piping tip, decorate the cooled cupcakes and top with optional garnish if desired.

Notes

The Secret to Perfect Texture: Fresh Carrots

For the best results, avoid pre-shredded, bagged carrots. These are often treated to stay dry in the bag, which will lead to a dry, crumbly cupcake. Instead, freshly shred or grate your carrots to get that essential moisture.

Customize Your Cupcakes: Mix-in Options

Feel free to make this recipe your own! You can gently fold in ½ cup of your favorite mix-ins to add extra texture and flavor. Some of my favorite additions include:

Crunchy Nuts: Chopped walnuts or pecans add a wonderful toasted flavor.
Sweet Chews: Raisins provide a nice burst of sweetness.
Tropical Twist: Shredded coconut flakes pair beautifully with the warm spices.

Success Tip: No matter which mix-ins you choose, wait until the very end to fold them in alongside the shredded carrots to avoid overmixing the batter!

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