Chocolate Paleo Cupcakes
5/5 - (1 vote)

These are the best paleo chocolate cupcakes I’ve ever had! They’re gluten-free and dairy-free, with a moist, rich crumb and delectable dark chocolate frosting.

This recipe comes together surprisingly quickly and easily. In short? They’re absolutely ideal.

Let’s be clear: this paleo cupcake recipe isn’t called “Best Chocolate Paleo Cupcakes Ever with Dark Chocolate Frosting (Gluten, Grain, and Dairy Free).”

It’s this:

Recipe for the Best Damn Chocolate Paleo Cupcakes Ever with Dark Chocolate Frosting (Gluten, Grain, Dairy-Free) That Could Fool Anyone Into Thinking They’re Made with White Flour, Sugar, and All Sorts of Unhealthy Stuff

They’re anything but foolproof. Alternatively, allow me to clarify. They’re both easy to make and completely capable of fooling even your most obstinate friends or family members.

You’ve seen them! Isn’t it true that everything healthy tastes bad? Yes, they, too. These chocolate paleo cupcakes will trick even them.

Grain-free, gluten-free, refined sugar-free, and dairy-free are all options.

They’re quite probably the best paleo thing I’ve ever eaten, with the moistest texture and perfect crumb, and that’s a huge claim!

Why is this recipe so delicious?

Chocolate Paleo Cupcakes Gluten-free
Food: Chocolate Paleo Cupcakes (Source: Pinterest)
  • They taste exactly like a chocolate cupcake from a bakery. Well, from a fantastic bakery.
  • The crumb has a delicate texture and is moist. They’re rich, chocolaty, and incredibly soft.
  • These paleo chocolate cupcakes are surprisingly simple to make and come together quickly.
  • This dish uses coconut sugar and is just sweet enough.
  • The dark chocolate frosting is quite simple to make!
  • The cupcakes are just rich enough and oh so moist thanks to the moderate baking temperature.

How do you make it?

It’s strangely simple and quick. Here’s how it’s done:

Preheat the oven to 325 degrees Fahrenheit.

In a large mixing bowl, whisk together all of the dry ingredients for the paleo cupcakes. Whisk together all of the wet ingredients for the paleo cupcakes in a medium mixing bowl. Stir the wet ingredients mixture into the dry ingredients until smooth and lump-free.

Cupcake liners, preferably parchment paper liners, should be used to line 12 cupcake tins.

Fill each liner about 3/4 full. Bake for 16-17 minutes, checking at 14-15 minutes, or until a toothpick inserted in the center comes out clean. It should have crumbs but not be coated, and the center should still be liquid.

Remove the cupcakes from the oven and set them aside for 5 minutes before removing them to cool completely on a wire rack.

To make the frosting, combine all frosting ingredients in a microwave-safe bowl and microwave for 60 seconds, stirring well after each burst.

Set aside until room temperature or chill until very firm but scoopable, once completely melted and smooth.

If preferred, cover totally cooled cupcakes with frosting and chocolate jimmies. For added fanciness, frost with a piping bag.

Can I use ______ flour instead of almond, coconut, or tapioca flour?

The combination of three distinct paleo flours is what makes them so delicious:

  • Almond meal
  • flour of coconut
  • Tapioca starch

It took several attempts to get the flour combination just right, absolutely rich and moist. As a result, I strongly advise you to stick to the flours specified in the recipe or seek out another recipe that meets your specific ingredient needs.

The most common request I see is a nut-allergy-friendly variation, so try searching for a cassava-flour-based chocolate paleo cupcakes recipe if that’s the case.

Frosting these paleo chocolate cupcakes

Here are two options: Using a tiny offset spatula or butter knife, frost your paleo cupcakes. To see a video on how below do that with this frosting, scroll down to the recipe.

Second option: fill a piping bag with the dark chocolate frosting and swirl as desired! This dark chocolate frosting is quite rich and chocolatey, and it contrasts beautifully with the milder cupcake.

As a result, I enjoy putting a thick layer of chocolate icing on these paleo cupcakes! Not only that, but they’re absolutely gorgeous. Don’t you agree?

Chocolate Paleo Cupcakes

Preparation time: 10 minutes
16 minutes to cook
1 hour cooling time
26 minutes total

No one would suspect this paleo, gluten-free, and dairy-free chocolate cupcakes are paleo, gluten-free, and dairy-free! A thick, dark chocolate icing coats the cake.


Dry Ingredients

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

Wet Ingredients

  • 2 eggs
  • 1/2 cup full-fat coconut milk whisked well
  • 1/3 cup cold or room temperature coffee see Note 1
  • 2 teaspoons vanilla extract
  • 1/4 cup + 2 tablespoons refined coconut oil melted
  • 1 teaspoon apple cider vinegar
  • 2 teaspoons chocolate extract see Note 2

Dark Chocolate Frosting

  • 2 cups vegan chocolate chips like Enjoy Life or Lily’s, see Note 3
  • 3/4 cup coconut cream just the solid white part of a can of coconut milk or cream
  • 1/4 cup refined coconut oil
  • 1 teaspoon vanilla extract

Instructions For Chocolate Paleo Cupcakes

Chocolate Paleo Cupcakes Healthy
Food: Chocolate Paleo Cupcakes (Source: Pinterest)
  1. Preheat the oven to 325 degrees F.
  2. Whisk together the dry ingredients in a large mixing bowl. Whisk together the wet ingredients in a medium bowl until smooth. Pour the wet ingredients mixture into the dry ingredients bowl and stir until smooth and lump-free.
  3. 12 cupcake liners, ideally parchment paper, should be lined in a muffin tray. Fill muffin tin 3/4 full with batter or use a dish.
  4. Bake for 16-17 minutes on the center rack. Don’t overcook. Starting at 15 minutes, check for doneness every minute by inserting a toothpick into the center of a cupcake. The toothpick should come out with crumbs on it, but not totally coated, as the middle should be liquid. Remove the pan from the oven as soon as the toothpick comes out looking like this (crumbs but not coated). Remove cupcakes and cool completely on a wire rack after 5 minutes.
  5. Make the frosting while the cupcakes are cooling. Combine all ingredients in a medium mixing bowl. Microwave in 60-second increments, stirring well after each, until all ingredients are completely melted and smooth. Allow to cool to room temperature before serving, or refrigerate until solid yet scoopable.
  6. When the cupcakes are totally cool and the frosting has set, frost them. If you’re not on a strict paleo diet, top with chocolate jimmies.


Note 1: Coffee pulls out the natural cocoa flavor in chocolate dishes, so use a little of your leftover morning brew in these paleo cupcakes! If you don’t have any coffee, water will suffice.

Note 2: I highly recommend adding the chocolate extract to enhance the chocolate flavor in a recipe like these paleo cupcakes. If you can’t locate chocolate extract, you can leave it out.

Note 3: I use Enjoy Life chocolate chips, which are made with cane sugar. You’ll want to use a different kind of chocolate chips if you’re truly paleo and don’t eat refined sugar. Lily’s is keto-friendly, with stevia and erythritol as sweeteners.

Soy lecithin is present in Lily’s. Pascha Organic 100 percent Cacao chips are a sugar-free solution.

If you go with this method, you’ll definitely need to sweeten the frosting; add coconut sugar to taste while the mixture is heated, and stir well to dissolve.

Nutrition Information

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