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These are the best chocolate paleo cupcakes ever! Gluten free and dairy free, they’re moist and rich with a soft crumb, and the dark chocolate frosting is oh so good. This recipe is surprisingly easy and quick to pull together. In short? They’re just perfect.

Closeup of chocolate paleo cupcake frosted with dark chocolate frosting with a bite taken out

Let’s be clear here: the title of this paleo cupcakes recipe is not “Best Chocolate Paleo Cupcakes Ever with Dark Chocolate Frosting (Gluten, Grain, Dairy Free).”

It’s this:

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

They’re the opposite of foolproof. Or, well, let me clarify. They’re both foolproof to make, and completely able to fool even the most difficult of your friends or family. You know the ones! That claim everything healthy tastes funny? Yeah, even them. Even they will be fooled by these chocolate paleo cupcakes.

Overhead shot of many chocolate paleo cupcakes frosted with dark chocolate frosting and one bite taken out of one

Which is really amazing, because why? Because they’re…

  • grain free,
  • gluten-free,
  • refined sugar-free, and
  • dairy free.

With the moistest texture and perfect crumb, they’re quite possibly the best paleo thing I’ve ever eaten, and that’s a seriously bold claim!

Why this recipe is so good

  • They taste just like a regular bakery chocolate cupcake. Well, from a really good bakery.
  • The texture is moist with a soft crumb. They’re rich and chocolatey and so tender.
  • These chocolate paleo cupcakes are surprisingly easy to make and super quick to bring together.
  • This recipe is just sweet enough and is made with coconut sugar.
  • The recipe for the dark chocolate frosting could not be easier!
  • The low baking temperature keeps the cupcakes just dense enough and oh so moist.

Chocolate paleo cupcakes with dark chocolate frosting close together at an angle

How to make it

It’s weirdly easy and quick. Here’s how you do it:

Preheat the oven to 325º Fahrenheit.

Combine all the dry ingredients for the paleo cupcakes in a large mixing bowl; whisk well. In a medium bowl, combine all the wet ingredients for the paleo cupcakes; whisk well. Stir the wet ingredients mixture into the dry and stir until completely smooth and free of lumps.

Line 12 cupcake tins with cupcake liners, ideally parchment paper liners. Fill each liner 3/4 of the way full. Bake for 16-17 minutes, checking at 14-15 minutes, or until a toothpick inserted into the center of a cupcake just comes out clean. It will have crumbs but should not be coated and look like the center is still liquid.

Remove from the oven and let sit for 5 minutes; remove cupcakes and let cool fully on a wire rack.

Make frosting: microwave all frosting ingredients together in 60-second bursts, stirring very well in between. Once totally melted and completely smooth, set aside until room temperature or chill until very firm but scoopable.

Frosted chocolate paleo cupcake with dark chocolate frosting in a swirl topped with chocolate jimmies

Frost completely cooled cupcakes with frosting and top with chocolate jimmies, if desired. Try using a piping bag to frost for extra fanciness!

Why these are the easiest cupcakes EVER:

Because literally ALL of the ingredients can 1) already be found in your pantry or 2) they’re sold at Thrive Market, which as you know, is my favorite place to get my pantry staples, non-toxic cleaning supplies, clean wine (I mean, hello), and so much more at 25-50% below retail price. They’re all about making healthy living easy and affordable for everyone. By offering the highest quality, healthy and sustainable products available for every budget, lifestyle, and geography, you can now shop for thousands of the best-selling organic foods and natural products right at your fingertips. And best yet? It’s all delivered right to your door.

Who is Thrive Market for? Everyone can find what they need at Thrive Market — because they’re just like your neighborhood grocery store. Whether you follow a specific diet like Keto, Paleo, Vegan, or are trying to make healthier decisions by shopping sugar-free, cholesterol free, high fiber, etc — Thrive Market is the place for you.

And because I love you, you can get an EXTRA 25% off your first order and a free 30 day trial by using my fancy, custom link:

Can I substitute _______ flour for the almond flour/coconut flour/tapioca flour?

What makes them oh so good is the combination of 3 different paleo flours:

It took multiple tries to get the flour combo just right, perfectly rich, perfectly moist. For this reason, I highly recommend you stick with the flours as listed in the recipe or try to find another recipe that suits your specific ingredient requirements. 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.

In fact, let me know on Instagram if you need a nut-free version, and I might just make a cassava-flour version myself!

Overhead shot of many chocolate paleo cupcakes frosted with dark chocolate frosting and one bite taken out of one

Frosting these chocolate paleo cupcakes

Two options here: frost your paleo cupcakes with a small offset spatula or butter knife. Scroll down to the recipe to watch a video on how to do that with this frosting.

Second option: fill a piping bag with this dark chocolate frosting and swirl to your heart’s content! This dark chocolate frosting is so dang chocolatey and rich, and I love how it pairs with the milder cupcake. For that reason, I love piping lots of chocolate frosting on these paleo cupcakes! Not only that, but they’re super stunning. Don’t you think?

Other recipes you’ll love:

5 from 29 votes

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

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


Dry Ingredients

  • 2 cups almond flour
  • ½ cup tapioca flour
  • 2 ½ tablespoons coconut flour
  • ½ cup coconut sugar
  • ½ cup cocoa powder or cacao powder
  • 1 teaspoon baking soda
  • ½ 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.

Approximate Information for One Serving

Calories: 429calProtein: 8gFat: 32gSaturated Fat: 17gCholesterol: 27mgSodium: 217mgPotassium: 134mgTotal Carbs: 36gFiber: 6gSugar: 19gNet Carbs: 30gVitamin A: 40IUVitamin C: 0.5mgCalcium: 90mgIron: 4.2mg
Nutrition Disclaimers
Number of total servings shown is approximate. Actual number of servings will depend on your preferred portion sizes.
Nutritional values shown are general guidelines and reflect information for 1 serving using the ingredients listed, not including any optional ingredients. Actual macros may vary slightly depending on specific brands and types of ingredients used.
To determine the weight of one serving, prepare the recipe as instructed. Weigh the finished recipe, then divide the weight of the finished recipe (not including the weight of the container the food is in) by the desired number of servings. Result will be the weight of one serving.

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  1. Avatar Emily Boronkay says:

    We made a double batch of these 2 weeks and 2 days ago baking some in mini Bundt pans. I found one in the fridge last night that had escaped notice. I expected it to be dry, but if anything it was better.
    This recipe is a keeper, the first I’ve ever printed out to keep.5 stars

    1. Megan | 40 Aprons Team Megan | 40 Aprons Team says:

      Oh wow, that’s truly impressive! Thank you so much, Emily!!

  2. Hello! I am excited to make this recipe. Is it a 1:1 substitution if I want to use whole milk and butter instead of the dairy free alternatives?

    1. Megan | 40 Aprons Team Megan | 40 Aprons Team says:

      Hi, Tatyana! So since these cupcakes were designed to be paleo, we actually haven’t tested this recipe with whole milk and regular butter, and we can’t say for sure how it’ll turn out with those substitutions. Subbing them 1:1 should work in theory, but we can’t guarantee it. If you give it a try with those ingredients, though, please let us know how it turns out!

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