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Paleo Apple Pie Cupcakes

These Paleo Apple Pie Cupcakes, are epically good! Each little cake is filled with apple pie filling, topped with honey butter frosting and a drizzle of caramel sauce.
Course Dessert
Prep Time 15 minutes
Cook Time 45 minutes
Total Time 1 hour
Servings 12



  • 3/4 cup almond flour
  • 1/3 cup + 3 tablespoons tapioca flour
  • 1/4 cup coconut flour
  • 11/2 teaspoons baking powder
  • 1/4 teaspoon sea salt
  • teaspoon ground cinnamon
  • 1/8 teaspoon nutmeg
  • 1/8 teaspoon ground ginger
  • 1/8 teaspoon ground cloves
  • 1/2 cup 1 stick grass fed unsalted butter, melted and cooled
  • 3/4 cup pure maple syrup
  • 2 large eggs whisked at room temperature
  • 1 teaspoons pure vanilla extract
  • 1/2 cup coconut cream

Apple Pie Filling:

  • 2 medium sized apples peeled, cored and diced
  • 2 Tbsp unsalted butter
  • ¼ cup coconut sugar
  • lemon juice from a quarter lemon
  • ½ Tbsp cinnamon
  • 1/8 teaspoon sea salt
  • 1/8 teaspoon ground nutmeg
  • 1/8 teaspoon ground ginger
  • 1/8 teaspoon ground cloves


  • 1 cup unsalted butter room temperature
  • 1/2 cup raw honey
  • 2 Tsp vanilla
  • 4 Tbsp tapioca flour or arrowroot flour
  • 4 Tbsp coconut flour
  • 1/4 tsp sea salt

Paleo Caramel Sauce:

  • 2 tablespoons water
  • 1/4 cup raw coconut sugar
  • 1/2 cup coconut milk
  • 1 teaspoon vanilla extract
  • pinch salt


Apple Pie Filling:

  1. In a nonstick skillet, melt 2 tablespoons butter over medium-high heat.
  2. Add apples; cook about 5 minutes, stirring occasionally, until softened. Sprinkle with 2 tablespoons coconut sugar, salt, cinnamon, nutmeg, ginger, and ground cloves.
  3. Cook for 5 minutes or until apples is tender.
  4. Squeeze in lemon juice and stir to combine.
  5. Set aside

Paleo Caramel Sauce:

  1. bring the water and coconut palm sugar to a boil stirring the mixture constantly
  2. add the coconut milk vanilla extract and salt and cook for 10-15 minutes over medium heat, stirring constantly so that it doesn't burn. The mixture will start to thicken and turn darker in color.
  3. Set aside


  1. Preheat the oven to 350° F degrees. Line a 12-cup cupcake/muffin pan with cupcake liners. Set aside.
  2. In a medium sized bowl, stir together the flours, baking powder, salt, and lemon zest until thoroughly combined. Set aside.
  3. In a large bowl whisk butter, maple syrup, eggs, vanilla and coconut cream together until smooth.
  4. Add the flour mix into the butter mix and stir until combined.
  5. Divide the batter between 12 liners in your cupcake pan. Bake for 18 minutes, or until a toothpick inserted in the center comes out clean. Allow to cool completely, then using a knife cut a square into the center of each cupcake and scoop out the center of the cupcake. Making a small well to place about 1 tablespoon of apple pie filling.


  1. In a mixing bowl, combine everything
  2. Blend with an electric mixer or hand mixer on medium until whipped together
  3. Put into a piping bag and top cupcakes.
  4. Pipe frosting onto each cupcake.
  5. Then drizzle paleo sauce over frosting. As much or as little as you like.
  6. Store any unused paleo caramel sauce covered in the refrigerator.

Recipe Notes

Frosting: Can be made ahead and stored in the refrigerator covered for up to 2-3 days. Bring to room temperature before frosting cupcakes.