You know those recipes that you grow up eating throughout your childhood and you continue to eat it into adulthood? This paleo cupcakes recipe is inspired by the Hershey’s Deep Dark Chocolate Cake recipe which has been a sweet treat in our household since I was a kid. My parents found it in a Hershey’s cookbook way back when and wrote it down on a recipe card which still exists to this day at my moms house.

It’s probably one of the best chocolate cake recipes I’ve ever known (also the batter is AMAZING – if that’s your thing), but now that I don’t eat gluten or dairy and I mostly follow the paleo diet, I figured I would try to re-create this recipe with healthy ingredients and without any grains, gluten or dairy.

I essentially took the original recipe and swapped out the ingredients 1-to-1 with paleo friendly ingredients. I also added a dairy free chocolate cream cheese frosting. What do you know, it turned out just as amazing!

Of the friends and family who have tried this *healthified* version of the recipe, they’ve all said that they would never guess that it was any different than regular cupcakes. For this reason, this is a great recipe for birthdays and other special occasions.

This recipe is paleo (if you omit the frosting), gluten-free, dairy free, low lectin, and can be made vegan, AIP, lower carb, elimination diet and candida diet friendly with the modifications listed below.

Product brands I recommend for this recipe

  • Prana organic cacao powder
  • Rogers icing sugar
  • Nutiva butter flavoured coconut oil
  • Soy free Earth Balance vegan butter
  • Bob’s Red Mill cassava flour
  • Daiya cream cheese
Chocolate cupcakes with chocolate frosting

Recipe ingredient substitutions:

Sugar substitutions: This recipe calls for coconut palm sugar, but you could also swap that out for cane sugar or brown sugar. You could also swap it out for a granulated sugar-free blend such as Swerve.

Dairy free milk substitutions: Any type of dairy free milk could be used for this recipe including coconut milk or coconut cream, almond milk, oat milk, cashew milk etc. If you tolerate dairy, you could also use regular cows milk.

Cacao powder substitutions: This recipe calls for raw cacao powder, but you could also use cocoa powder. Read more about the difference between cacao powder vs cocoa powder. For some extra pizzazz you could also add some additional dairy free chocolate chips to make double chocolate cupcakes!

White vinegar substitutions: You may be wondering why the white vinegar in this recipe. This is to emulate the taste of buttermilk which is essentially soured milk. Because this recipe does not include dairy, I’ve added white vinegar to the dairy free milk to make it more like buttermilk. I know it sounds weird and crazy, but trust me. The flavour it adds is unreal.

Cassava flour substitutions: Cassava flour is the most similar to white flour, and for this reason I wouldn’t recommend subbing the flour out for any other grain free flour. However, if you don’t have cassava flour, you could also use tapioca flour, arrowroot starch, or potato starch because they are the most similar to cassava flour.

Coconut oil substitutions: Instead of coconut oil, you could swap it out for vegan butter or any other type of cooking oil or fat.

Dietary modifications:

Make this recipe lower calorie/fat: Reduce the amount of coconut oil to ¼ cup and increase the amount of dairy free milk to 1 ¼ cups.

Make this recipe vegan: Swap of the eggs for egg substitutes such as flax eggs, gelatin eggs or chia eggs.

Make this recipe candida diet friendly: Swap out the sugar for a granulated or powdered sugar-free alternative such as erythritol or stevia. Make sure to use an unsweetened dairy free milk such as almond milk. Omit the vinegar. There are mixed opinions on whether cassava flour is candida diet friendly, but I have found personally that it does not aggravate my symptoms. Give it a try and see how it goes! Omit the frosting since there may be ingredients in the dairy free cream cheese and vegan butter that are not suitable.

Make this recipe AIP friendly: Swap out the eggs for gelatin eggs. Use coconut milk for the dairy free milk. Use carob powder instead of cacao powder. Omit the frosting.

Make this recipe elimination diet friendly: Swap out the eggs for egg substitutes such as flax eggs, gelatin eggs or chia eggs. If the elimination diet you are following cuts out chocolate, use carob powder instead of cacao. Omit the frosting since there may be ingredients in the dairy free cream cheese and vegan butter that are not suitable.

Make this recipe lower carb/sugar: Instead of using cassava flour, try using a mixture of almond flour and coconut flour. Instead of using coconut sugar, use a sugar-free alternative such as swerve for the batter and frosting.

Looking for more healthy recipes and meal plans?

If you are looking for more healthy recipes and meal plans, check out my premade meal plans and recipe books (which come with 140 recipes for breakfasts, lunches, dinners, snacks & desserts).

Tried my paleo chocolate cupcake recipe?

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You might also like: 

If you liked these healthy chocolate cupcakes, you might like my other cassava flour recipes:

If you are looking for more, download my free 7 day paleo meal plan!

Cassava Flour Chocolate Cupcakes + Dairy Free Chocolate Cream Cheese Frosting

Tara Klippert
This recipe is dairy free, gluten free, paleo, grain free, and soy free.
5 from 6 votes
Prep Time 30 minutes
Cook Time 25 minutes
Total Time 55 minutes
Course Dessert
Cuisine American
Servings 24
Calories 255 kcal


Dairy free chocolate cream cheese frosting


  • Take the vegan cream cheese and vegan butter out of the fridge and let it soften on the counter until it is room temperature.
  • Preheat your oven to 325 degrees F.
  • Then in a stand mixer or large bowl, mix your dry ingredients including cacao powder, baking powder, baking soda, cassava flour and salt together.
  • In a separate small bowl, cream together the sugar and coconut oil.
  • Then mix the remaining ingredients including eggs, vanilla, dairy free milk and white vinegar into the sugar/oil mixture.
  • Then combine both the dry and wet ingredients together and mix in the stand mixer until thoroughly combined.
  • Once your batter is thoroughly mixed, add the hot water to the chocolate mixture and continue mixing until fully incorporated.
  • Now you are ready to distribute the batter evenly into 24 muffin tins lined with parchment muffin cups.
  • Bake the cupcakes for 20 to 25 minutes or until the toothpick test comes out clean.
  • While your cupcakes are baking, beat together the vegan cream cheese with vegan butter and vanilla. Then add the cacao powder and slowly start adding the icing sugar while mixing. Beat until smooth. If the icing looks too thin you can add extra icing sugar.
  • Once the cupcakes are cooked, place them on a wire rack and allow them to cool completely.
  • Using your piping set (or a knife or spoon), top the cupcakes with the vegan chocolate frosting.
  • Keep your cupcakes in an airtight container in the fridge until ready to serve.



Serving: 1servingCalories: 255kcalCarbohydrates: 42.7gProtein: 2.2gFat: 9.2gSaturated Fat: 6gPolyunsaturated Fat: 0.7gMonounsaturated Fat: 1gCholesterol: 15.5mgSodium: 429.7mgPotassium: 346.8mgFiber: 2.3gSugar: 29.8g
Keyword dairy free, gluten free, paleo, soy free
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Tara Klippert
About the author Tara Klippert

Tara Klippert is a Registered Health and Nutrition Counselor and holds a diploma in Holistic Nutrition and Health Coaching. She shares her gluten free, dairy free & allergy friendly recipes.