Go Back
+ servings
Closeup of chocolate paleo cupcake frosted with dark chocolate frosting with a bite taken out

Best Chocolate Paleo Cupcakes Ever with Dark Chocolate Frosting (Gluten Free, Dairy Free)

Perfect, moist, tender chocolate cupcakes that no one would guess are paleo, gluten free, and dairy free! Topped with a rich, dark chocolate frosting.
Course Dessert
Cuisine American
Keyword chocolate, cupcakes, paleo
Prep Time 10 minutes
Cook Time 16 minutes
Cooling Time 1 hour
Total Time 26 minutes
Servings 12 cupcakes
Calories 429kcal


Dry Ingredients

  • 2 cups almond flour
  • 1/2 cup tapioca flour
  • 2 1/2 tablespoons coconut flour
  • 1/2 cup coconut sugar
  • 1/2 cup cocoa powder or cacao powder
  • 1 teaspoon baking soda
  • 1/2 tsp salt

Wet Ingredients

Dark Chocolate Frosting


  • Preheat oven to 325º Fahrenheit.
  • In a large bowl, whisk together dry ingredients. In a medium bowl, whisk together wet ingredients until smooth. Pour wet ingredients mixture to dry ingredients bowl and stir until well combined and with no lumps.
  • Line muffin tin with 12 cupcake liners, preferably parchment paper. Pour or use a disher to fill muffin tin 3/4 full.
  • Bake in the middle rack for 16-17 minutes. Do not overbake. Begin checking for doneness every minute starting at 15 minutes: insert a toothpick into the center of a cupcake. The toothpick should come out with crumbs but not completely coated like the center is liquid. As soon as the toothpick comes out this way (Crumbs but not coated), remove the pan from the oven. Let sit 5 minutes then remove cupcakes and cool completely on a wire rack.
  • While cupcakes cool, make the frosting. In a medium bowl, combine all ingredients. Microwave in 60-second bursts, stirring very well in between each burst, until ingredients are completely melted and totally smooth. Set aside and let cool to room temperature or chill in the refrigerator until firm but scoopable.
  • Frost cupcakes when cupcakes are completely cool and frosting is set. Sprinkle with chocolate jimmies, if desired and not on a strict paleo diet.



Note 1
Coffee brings out the natural cocoa flavor in chocolate dishes, so I highly recommend using a bit of your leftover morning brew in this paleo cupcakes recipe! However, if you don't have coffee on hand, water will do.
Note 2
Chocolate extract is another amazing way to enrich the chocolatey flavor in a recipe like these paleo cupcakes, so I highly recommend using it. However, you can omit the chocolate extract if you cannot find it.
Note 3
I use Enjoy Life chocolate chips, which do have cane sugar as an ingredient. If you are very strictly paleo and do not consume any refined sugar, you will want to use a different brand of chocolate chips. Lily's is keto-friendly and sweetened by stevia and erythritol. Lily's does contain soy lecithin. For an unsweetened option, try Pascha Organic 100% Cacao chips. You will absolutely need to sweeten the frosting if you go this route, though; try adding coconut sugar to taste when the mixture is warm and stirring to dissolve well.


Calories: 429kcal | Carbohydrates: 36g | Protein: 8g | Fat: 32g | Saturated Fat: 17g | Cholesterol: 27mg | Sodium: 217mg | Potassium: 134mg | Fiber: 6g | Sugar: 19g | Vitamin A: 40IU | Vitamin C: 0.5mg | Calcium: 90mg | Iron: 4.2mg | Net Carbs: 30g