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Gluten Free Carrot Cake Cupcakes with Cream Cheese Frosting

Sandi Gaertner
An easy gluten free carrot cake cupcake recipe with a cream cheese frosting.
4.84 from 12 votes
Prep Time 15 mins
Cook Time 22 mins
Total Time 37 mins
Course Gluten Free Dessert Recipes
Cuisine American
Servings 12 cupcakes
Calories 364 kcal



  • 1 ½ cups gluten free flour blend * see note
  • ½ cup almond milk * see note
  • 1 ½ cups shredded carrot
  • 1 teaspoon baking powder
  • teaspoon salt
  • ¼ teaspoon ground allspice
  • ½ teaspoon ground nutmeg
  • 1 ½ teaspoon ground cinnamon
  • 1 ¼ cups coconut sugar
  • 3 large eggs
  • ¼ cup coconut oil
  • 3 ounces apple sauce
  • 3 tablespoons chia seeds

For Frosting

  • 8 ounces softened cream cheese * see note
  • ¼ cup softened butter
  • 1 teaspoon pure vanilla extract
  • 2 cups powdered sugar


  • Preheat the oven to 350º F.
  • In a large bowl, add all of the dry ingredients and whisk to blend.
  • Grate carrots with a grater, or a food processor.
  • Add wet ingredients to a bowl. Mix well then add carrots and mix to blend.
  • Pour the wet ingredients into the dry ingredients and mix.
  • Add paper cupcake liners to a muffin tin and fill each ¾ with the cake batter.
  • Bake for 20-25 minutes.
  • Remove from the oven and take cupcakes out of the muffin tin. Put them on a cooling rack and allow them to cool all of the way.
  • In a mixer, add all frosting ingredients and mix until fluffy.
  • Put the frosting into a frosting bag and squeeze the frosting out onto each cupcake.
  • *Optional: sprinkle coconut on top of each cupcake.


  1. I have tested this recipe with King Arthur Measure for Measure GF, Bob's Red Mill 1 to 1 GF blend, and Authentic Foods Multi Blend. That doesn't mean others will not work, I just have not tested other flours.
  2. If your gluten free flour blend doesn’t contain Xanthan Gum or Guar Gum, please add 1 teaspoon.
  3. To make this recipe dairy-free, substitute the butter for vegan butter and use a dairy-free cream cheese like Kite Hill.
  4. Do not use imitation vanilla.
  5. I highly suggest using almond flour and not almond meal. Almond meal is more coarse and will make your donuts grainy.
  6. Other dairy-free kinds of milk will work but I do not recommend canned coconut milk.
  7. If you want your cupcakes to have a domed style top, bake at 425º F for the first 5 minutes then reduce the temperature to 350º F.
  8. These cupcakes will keep up to 4 days in an air-tight container, or up to 4 months in the freezer.


Serving: 1gCalories: 364kcalCarbohydrates: 50gProtein: 5gFat: 18gSaturated Fat: 10gCholesterol: 72mgSodium: 193mgPotassium: 144mgFiber: 3gSugar: 33gVitamin A: 3104IUVitamin C: 1mgCalcium: 89mgIron: 1mg
Keyword gluten free carrot cake cupcake recipe, gluten free carrot cake cupcakes, gluten free carrot cupcakes
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