Paleo Chocolate Cupcakes

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Make these fudge-y chocolate cupcakes during your next chocolate craving!

I have to admit, as far as the chocolate vs. vanilla debate goes, I almost always trend vanilla.

Yeah, yeah, there are all sorts of hilarious connotations there about me being boring and basic, in the kitchen and in certain other rooms I won’t mention.

That said, I am by no means a chocolate hater (if such a thing even exists.) At the end of the day, I’m a sweet tooth first. And while I may love vanilla, I am not immune to occasional chocolate cravings.

When those cravings hit, nothing hits the spot quite like a chocolate cupcake. Between moist chocolate cake and rich creamy frosting, cupcakes feature chocolate in two of its best forms.

However, like so many of us, I also happen to be a health and figure-consicous sweet tooth. Fortunately, chocolate is one of the easier sweets to enjoy on the lighter side. As you’ve probably heard, chocolate (especially of the dark variety) is naturally rich in antioxidants, which makes this treat a relatively healthy option to turn to when it comes to satisfying cravings.

Moreover, when it comes to baking, chocolate is a great ally to have on your ingredients list. Not only does cocoa powder help reduce the amount of flour you need, but chocolate’s naturally rich flavor means you don’t have to rely as heavily on sugar and other sweeteners.

Finally, people have been enjoying chocolate for a long time, meaning it’s paleo friendly…at least in some of its forms. Milk chocolate truffles your coworker brought to the office? Not paleo. But unsweetened cocoa powder is a guilt-free ticket to paleo chocolate cupcakes.

Like many paleo recipes, these paleo chocolate cupcakes rely on a number of substitutions for typical baking ingredients. But don’t worry, I promise they will come out just as rich and chocolatey as the old-school version.

For this recipe, we’ve used almond flour for a great, grain-free flour substitute. This recipe also uses coconut oil and unsweetened applesauce to substitute for traditional liquid fats like butter. If you’ve never used applesauce in your baking before, this may sound a little weird, but don’t worry. This ingredient, especially when unsweetened, is for texture and consistency purposes only, it won’t affect the taste.

It will, however, provide a slight hint of natural sweetness, which we’ll enhance with coconut sugar. In place of the milk that cupcake recipes usually call for, this recipe suggests strong coffee, which, as any mocha lovers know, makes for a fantastic flavor combination. However, if you haven’t caught the java bug, feel free to just sub in some almond milk instead.

Finally, this recipe uses a rich and creamy three-ingredient frosting. To keep things paleo, I recommend Enjoy Life Semisweet Chocolate Chips. They’re your best source for non-GMO, vegan and paleo-friendly chocolate. Along with the chocolate, this frosting gets its rich and creamy texture from coconut milk. I recommend Native Forest for a simple, organic canned option.

Whether you’re paleo part-time, full-time, or just generally health conscious, these paleo chocolate cupcakes are a perfect go-to when you’re craving some quality chocolate indulgence.

And if you have more paleo chocolate cravings to satisfy, you’ll love these Paleo Fudge Brownies.

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Paleo Chocolate Cupcakes

These incredibly delicious cupcakes are made with clean ingredients that fit right in with your healthy eating lifestyle.
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Yield 12 people
Serving Size 1 cupcake
Course Dessert
Cuisine American
Author SkinnyMs.


For the Cupcakes

  • 3/4 cup cocoa powder
  • 1 cup almond flour
  • 1 1/2 teaspoons baking powder
  • 1/4 teaspoon kosher salt
  • 1/2 cup coconut oil melted
  • 1/2 cup applesauce unsweetened
  • 1/2 cup coconut sugar
  • 4 egg whites
  • 1/4 cup strong brewed coffee or 1/4 cup almond milk
  • 1 tablespoon vanilla extract

For the Frosting

  • 2 cups semisweet chocolate chips
  • 1/2 cup coconut milk canned
  • 1/2 teaspoon almond extract or substitute any flavor such as orange, vanilla, or raspberry


For the Cupcakes

  • Preheat your oven to 350 and line a muffin pan with paper liners or spray with nonstick spray. Set aside.
  • In a medium mixing bowl, stir together the cocoa powder, almond flour, baking powder, and salt. Set aside.
  • In a large mixing bowl, stir together the melted coconut oil, applesauce, coconut sugar, eggs, coffee, and vanilla. Gradually add the dry mixture to the wet and stir just until combined. If batter is too runny, add additional almond flour as needed. Spoon the batter evenly into the muffin liners, about 3/4 full.
  • Bake for 25 to 30 minutes. A toothpick inserted in the middle should come out mostly clean. There should be a few crumbs stuck to the tooth ick.
  • Let cool for 5 minutes and then remove to a wire rack to cool completely. Let set for about 2 hours or until completely cool.

For the Frosting

  • Add all ingredients to a small saucepan, heat to low, and stir until chocolate chips are melted. Allow to cool before spreading over cupcakes. Store frosted cupcakes in an airtight container in the refrigerator.

Nutrition Information

Serving: 1cupcake | Calories: 333kcal | Carbohydrates: 30g | Protein: 4g | Fat: 24g | Saturated Fat: 15g | Sodium: 109mg | Fiber: 3g | Sugar: 25g |
SmartPoints (Freestyle): 17
Keywords dairy-free, Gluten-Free, Paleo, Vegetarian

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The SkinnyMs. team believes that all people, regardless of age, size, and fitness level, have the power to transform their lives — they just need the resources to do so. The SkinnyMs. method promotes healthy living through a combination of clean eating and regular exercise. We offer everything you need to be successful.

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    1. Julie, Honey was in the directions by mistake, it has been removed. 1/2 cup coconut sugar is the sweetener. 🙂

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