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Paleo Carrot Cake Cupcakes with Cream Cheese Frosting

Moist gluten free carrot cake cupcakes topped with creamy, tangy cream cheese frosting. Packed with pineapple, pecans, spices, and carrots, like a traditional carrot cake, but gluten free, grain free, refined sugar free, and with a dairy free option.
Course Dessert
Cuisine American
Keyword carrot cake, cupcakes, paleo
Prep Time 10 minutes
Cook Time 20 minutes
Cooling Time 30 minutes
Total Time 30 minutes
Servings 12 cupcakes
Calories 296kcal


  • 2 large eggs
  • 1/2 cup coconut sugar
  • 1/3 cup refined coconut oil melted
  • 2 teaspoons vanilla extract
  • 1 8- oz. can crushed pineapple in juice drained, about 1 cup
  • 1 1/2 cup grated carrots
  • 1 1/2 cups almond flour
  • 2 tablespoon coconut flour
  • 2 tablespoon tapioca flour
  • 1 teaspoon baking soda
  • pinch salt
  • 1/2 teaspoon cinnamon
  • 1/4 teaspoon ground ginger
  • 1/2 cup chopped pecans

Cream Cheese Frosting

  • 8 ounces cream cheese or dairy-free cream cheese softened, see Note 1
  • 1/4 cup pure maple syrup
  • 1/4 cup refined coconut oil softened
  • 1/2 teaspoon vanilla extract
  • pinch ground ginger


  • Preheat oven to 350º F. Line a muffin tin with 12 paper liners, preferably parchment paper liners.
  • In a large bowl, whisk eggs. Stir in coconut sugar, melted coconut oil, and vanilla extract. Stir together until well combined. Add in drained crushed pineapple, carrots, and dry ingredients: almond flour, coconut flour, tapioca flour, baking soda, salt, cinnamon, and ginger. Whisk well until well combined and smooth, then fold in chopped pecans.
  • Portion out batter into lined cupcake tin, filling each completely full. Recipe will make approximately 11-12 cupcakes. Bake on the middle rack for 20-25 minutes or until a toothpick inserted into the middle comes out clean. Remove from the oven and let cool for a few minutes, then remove cupcakes from the tin and let fully cool on a wire rack.
  • In the meantime, make your cream cheese frosting. Combine softened cream cheese, maple syrup, softened coconut oil, vanilla extract, and ground ginger in a medium bowl. Beat with a stand or handheld mixer until completely smooth. Set aside.
  • When cupcakes are completely cool, frost with an offset spatula or butter knife. You can also pipe a swirl onto the top of the cupcake then smooth with a spatula or butter knife. Garnish with a sprinkle of finely chopped pecans, if desired.



Note 1
For dairy-free cream cheese, I like Kite Hill and Miyoko's. If you are paleo but eat some dairy, try a cultured dairy cream cheese like Nancy's! I definitely recommend the dairy version of this frosting if you tolerate it.
Note 2
To test cupcakes for doneness, insert a toothpick into the center of a cupcake. The toothpick should come out clean with a few crumbs.
Note 3
I love parchment paper cupcake liners because they're so reliably nonstick. In fact, they're so nonstick that they have a little trouble staying on these muffins. If you're displaying or transporting these, you might want to use regular paper muffin liners here.
Note 4
For the frosting, make sure the coconut oil is quite soft. Otherwise, you will have a lumpy frosting full of little beads of solidified coconut oil. Using melted to make the frosting is OK, so long as you give the frosting plenty of time to solidify before frosting.


Calories: 296kcal | Carbohydrates: 21g | Protein: 5g | Fat: 22g | Saturated Fat: 8g | Cholesterol: 48mg | Sodium: 189mg | Potassium: 147mg | Fiber: 3g | Sugar: 13g | Vitamin A: 2975IU | Vitamin C: 3mg | Calcium: 71mg | Iron: 1mg | Net Carbs: 18g