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Gluten Free Carrot Cake Cupcakes with the Best Cream Cheese Frosting

  • Author: Mia Swinehart
  • Prep Time: 15 minutes
  • Cook Time: 17 minutes
  • Total Time: 32 minutes
  • Yield: 12 muffins 1x
  • Category: Dessert, Snacks


Moist and flavorful gluten free cupcakes with a simple cream cheese frosting!


  • 1/3 cup butter, melted (or sub coconut oil) ⠀
  • 2 large eggs ⠀
  • 1/3 cup maple syrup ⠀
  • 1/4 cup coconut sugar ⠀
  • 1/4 cup plain or vanilla greek yogurt (can sub dairy free yogurt or sour cream)
  • 1 tsp vanilla extract
  • 1 + 1/2 cups finely grated carrots (from ~2-3 carrots_
  • 1 + 1/3 cup Bob’s Red Mill Super Fine Almond Flour
  • 1/3 cup + 3 tbsp oat flour ⠀
  • 1/3 cup gluten free old-fashioned rolled oats
  • 1 + 1/2 tsp cinnamon
  • 1/2 tsp nutmeg ⠀
  • 3/4 tsp sea salt ⠀
  • 1 tsp baking soda ⠀
  • Optional add ins: raisins, pecans

For the Cream Cheese Frosting

  • 8 oz cream cheese, softened*
  • ¼ cup maple syrup
  • 1 tsp vanilla extract


  1. Preheat oven to 350°F and line 12 muffin tins with cupcake liners.
  2. In a large bowl, whisk the butter, eggs, maple syrup, coconut sugar, yogurt, and vanilla until smooth. Stir in the shredded carrots.
  3. Mix in the remaining dry ingredients, and stir until a smooth batter forms. If adding, fold in your pecans and/or raisins here.
  4. Scoop the batter into 12 muffin tins.
  5. Bake for 16-18 minutes, until a toothpick comes out mostly clean. Allow to cool.
  6. While muffins are cooling, use a hand mixer to beat the cream cheese until smooth, then add in the maple syrup and vanilla and mix until well-combined. Set in refrigerator until muffins are cool. Once muffins are frosted, store in the refrigerator for up to 6 days.


*While technically you can use dairy free cream cheese, for the best flavor results I really recommend a regular cream cheese here!