Paleo Chocolate Cupcakes


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Paleo chocolate cupcakes are extremely moist, decadent and rich, with a perfectly fluffy texture. You’ll never know they’re gluten-free and dairy-free! Top them off with a swirl of my vegan chocolate buttercream frosting for one irresistible treat.

Paleo chocolate cupcakes on a table.

Let me start off by introducing my most loved paleo chocolate cake recipe. If you’ve made the cake before, you know what I’m talking about. It has all the delicious textures and flavors of a real chocolate cake, while being gluten-free, dairy-free and paleo. It’s a reader favorite with over 1000 comments.

And many of you have asked if that cake can be turned into cupcakes. The answer? Oh yes, it sure can.

These cupcakes are simply half of that cake recipe. But for those who don’t want to do the math on the ingredients, no worries, I’ve done it for you. These cupcakes are just as light, fluffy, and perfectly moist as the original cake…in smaller cupcake form. Let’s dive in.

Ingredients for making paleo chocolate cupcakes.

Paleo Chocolate Cupcake Ingredients

I go into detail on why each of these ingredients is critical to the success of this recipe on the original cake post. So if you’d like more information check that out. But here’s what you’ll need for the cupcakes:

Dry ingredients

  • Almond Flour – 1 1/2 cups
  • Tapioca Flour – 1/2 cup
  • Coconut Flour – 2 tablespoons
  • Coconut Sugar – 1 cup
  • Raw Cacao Powder – 3/4 cup
  • Baking Soda – 1 teaspoon
  • Espresso Powder – 1/2 teaspoon
  • Salt – 1/2 teaspoon

Wet Ingredients

  • Eggs – 2 large eggs
  • Full-Fat Coconut Milk – 3/4 cup
  • Water – 1/2 cup
  • Coconut Oil – 1/4 cup
  • Apple Cider Vinegar – 1/2 tablespoon
  • Vanilla Extract – 1 teaspoon

Chocolate Buttercream Ingredients

  • Powdered Sugar – 4 cups (or powdered coconut sugar for added richness)
  • Cacao Powder – 1/2 cup
  • Organic Palm Shortening – 1/2 cup (or vegan butter)
  • Dairy-Free Milk – 1/3-2/3 cup
  • Vanilla Extract – 1 teaspoon

Filling the cupcake pan with chocolate batter.

How To Make Paleo Chocolate Cupcakes

To get started, you’ll need to create the cupcake batter. Watch the video on my cake recipe to see how I do it, or follow these steps:

  1. Preheat your oven to 350 degrees Fahrenheit.
  2. Mix the dry ingredients. Add everything into a large mixing bowl and give it a good whisk.
  3. Mix the wet ingredients in a separate bowl. Then pour the wet mixture into the dry and whisk together for 1-2 minutes to create the batter.
  4. Prepare the cupcakes. Line a muffin tin with muffin cups and evenly divide the batter between 14 muffin cups.
  5. Bake for 25-28 minutes. Test to see if the cupcake is done using the toothpick test.
  6. Let the cupcakes cool. This is key if you’re layering frosting on top. If not, you can also eat them as little chocolate muffins!

Piping the chocolate buttercream frosting on the cupcakes.

How To Make Vegan Chocolate Buttercream Frosting

As your cupcakes are cooling, make the buttercream frosting. Then you can get to the piping fun!

  1. Blend all the ingredients in a mixer. Add the ingredients to a stand mixer and blend on low for 30 seconds. Then slowly increase the speed to high and blend for one minute.
  2. Test the frosting consistency. If your frosting is too thick, add more milk. If it’s too thin, add more powdered sugar.
  3. Pipe the cupcakes. Place the frosting into a piping bag and pipe swirls on top of each cupcake.

Paleo chocolate cupcakes on a table.

Unwrapping a paleo chocolate cupcake.

Can You Make the Cupcakes Ahead of Time?

Absolutely! You can make the cupcakes up to two days before a party or event. Let them cool completely, then store in an airtight container at room temperature on your counter.

You can also make the frosting ahead of time and store in a separate container in the fridge. Just re-whip the frosting before placing in a piping bag. I prefer to store the cupcakes unfrosted and frost right before serving for the most fresh texture. But you could store them frosted as well.

Can you freeze cupcakes? You sure can. If you plan to eat them within a couple of weeks, I just frost and store in an airtight glass storage container. If you plan to store them longer (up to 2 months), you can prevent freezer burn by wrapping the unfrosted cupcakes in plastic wrap before storing in an airtight glass container. And let me tell you, defrosting chocolate cupcakes is mighty tasty meal prep!

Biting into a paleo chocolate cupcake.

More Decadent Chocolate Recipes

If you’ve got some cacao powder leftover, here’s a few of my favorite chocolate recipes to whip up!

Paleo Chocolate Cupcakes (gluten-free, dairy-free)

5 from 32 votes
Prep: 30 minutes
Cook: 30 minutes
Total: 1 hour
Servings: 14 servings
Author: Lisa Bryan


Paleo chocolate cupcakes are extremely moist, decadent and rich, with a perfectly fluffy texture. They're gluten-free and dairy-free!


Cake Dry Ingredients

Cake Wet Ingredients

Vegan Chocolate Buttercream Frosting


Paleo Chocolate Cupcakes

  • Preheat your oven to 350 degrees fahrenheit.
  • Add all the dry ingredients into a large mixing bowl and whisk together.
  • Add all the wet ingredients to another bowl and stir together. Then pour the wet mixture into the dry and whisk together for one minute to create the batter.
  • Line muffin tins with muffin cups and evenly divide the batter between 14 muffin cups.
  • Bake for 25-28 minutes, or until a toothpick comes out clean.
  • Let the cupcakes cool completely before piping the frosting on top.

Vegan Chocolate Buttercream Frosting

  • Add all the ingredients to a stand mixer and blend on low for 30 seconds. Then slowly increase the speed to high and blend for one minute.
  • If you're mixture needs to be thinned out, add more milk. If you need to thicken, add more powdered sugar.
  • Once the cupcakes are completely cool, place the frosting into a piping bag and pipe swirls onto each cupcake.

Lisa's Tips

  • This recipe creates 14 full cupcakes (I fill each cupcake about 80% of the way full with batter). But you can create 15 slightly smaller cupcakes as well.
  • My baking time of 25-28 minutes is based on a standard oven. I'd recommend checking the cupcakes earlier, at 20 minutes if your oven tends to cook fast or if you're using a convection oven.
  • Remember to make sure your cupcake is 100% cool before frosting. Otherwise the heat from the cupcake will melt your frosting.
  • This is the brand of espresso powder that I use.


Calories: 410kcal | Carbohydrates: 56g | Protein: 5g | Fat: 22g | Saturated Fat: 9g | Cholesterol: 23mg | Sodium: 202mg | Potassium: 160mg | Fiber: 4g | Sugar: 42g | Vitamin A: 56IU | Vitamin C: 1mg | Calcium: 49mg | Iron: 2mg
Course: Dessert
Cuisine: American
Keyword: gluten free chocolate cupcakes, Paleo chocolate cupcakes
Did you make this recipe?Mention @downshiftology or tag #downshiftology!

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About the author

Lisa Bryan

Lisa is a bestselling cookbook author, recipe developer, and YouTuber (with over 2.5 million subscribers) living in sunny Southern California. She started Downshiftology in 2014, and is passionate about making healthy food with fresh, simple and seasonal ingredients.

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Recipe Rating


  1. Hi, These cupcakes are the best of the best and I have tried many many for the last 2 years. Everyone MUST try, “great” is not even enough to describe them.  

    Just 1 question, I have been searching for a good paleo vanilla cupcake (moist, fluffy, light) recipe but just can’t seem to find it. Is there anyway I can convert your chocolate cupcake to vanilla cupcake? What do I need to change? PLS HELPPPPP, thanks :)

      1. Yes ! I’d be very interested in a vanilla GF cupcake. These chocolate ones were delicious!5 stars

  2. This was soooo amazing!!!! I’m a total chocolate lover and love, love, love chocolate cake! I made this for our nephew-in-law, who is gluften-free, and also along with the pumpkin cake last night, and again, simply delicious! My husband loved how the house smelled as I was baking these cakes! All of the gf and non-gf people loved these recipes! Thank you!

  3. Hi Lisa, I don’t have a stand up mixer.  Do you think an immersion blender will work okay for the frosting? A friend made the paleo chocolate cake for my birthday last May and I am going to attempt these cupcakes for her birthday next Sunday. Wish me luck 🍀 

      1. Yes! It worked out so well. These are delicious.  And perfect for my friend who has gluten allergy.  Thanks Lisa ❤️5 stars

  4. Hi Lisa,

    I want to make these, do you think it would be okay to put it in a Bundt pan, and if so what size.  Love the blueberry cupcakes.

    Thanks in advance 

  5. Excited to try these, Lisa!! Do you think it would be fine to add chocolate chips into the cupcake batter? I’d like them to be a little more brownie like if possible…

  6. Made these for the first time with the help of my little niece and nephew. Their mom is GF; my niece is DF. The whole family was impressed with how good these were! The taste and texture were perfect. Ended up sharing this recipe with others. 5 stars

  7. Hello, just made this cupcakes and is it just me or it’s really a bit bitter than a regular chocolate cupcake?

    1. These cupcakes aren’t as sweet as your traditional chocolate cupcakes. Also, the cacao powder is not as sweet.

  8. I’ve made this recipe twice before and I love it. Do you think I can omit the chocolate and espresso to make vanilla cupcakes and if so would I have to make a lot of tweaks?5 stars

    1. Unfortunately, I don’t think that will work, as I’ve tested that on my chocolate cake version. But, I hope to create a vanilla version in the future :)

  9. Hi Lisa, the Cacoa powder I have says not to heat it, only to use it in raw desserts (to retain nutritional value) but other than that it’s ok to heat it? 

    1. Hi Rebecca – yes, that’s true. But the way I see it, we’re not really eating cupcakes for their nutritional value, so it’s all good – ha!

      1. Made these today, used cow’s milk because we ran out it coconut milk. It’s yummy!5 stars

  10. I made this recipe for a women’s group. The birthday girl is strict paleo. She was ecstatic.Most people ate two! I seriously couldn’t tell that this wasn’t a traditional white flour cupcake. The texture and taste was spot on! Thank you!5 stars

  11. I’ve been making all of the muffins and desserts from your recipe catalog and so far have loved them all!
    I have a Doc in my office that is dairy-free. I’m wondering if there is a way to make these cupcakes and this icing vanilla flavor instead of chocolate? I’m new to baking in general so if it’s as simple as removing the cocoa powder, sorry in advance for my lack of knowledge. Thank you for sharing such great recipes!5 stars

    1. Happy to hear you’ve been enjoying all my desserts so far! I haven’t made a vanilla version yet, but that is definitely on my to-do list!

  12. I made this for my daughter’s birthday. It was so good! It was my first time making a decadent treat since going paleo a year and a half ago- thank you for the recipe! It’s a keeper.5 stars

    1. Wow, I can’t believe this was your first dessert since last year! I’m glad you loved these cupcakes. Next up, you’ll have to try my paleo chocolate cake as well :)

  13. Great recipe!  I’ve made the cupcakes 3 times.  I have a *slight* problem with them falling in the middle.  We’re at 5,2k elevation and think it has to do with that.  I’ve found some adjustments for elevation, but it didn’t seem to make a difference.  Frosting covers it up, so really not a big deal, but was curious if you have suggestions.  5 stars

    1. Hi Alyssa – high altitude can definitely affect baking. Unfortunately, I’m not very well versed on baking at altitude as I’m at sea-level. Sorry!

  14. Hi! I would love to try these but would it be possible to replace the coconut sugar with brown sugar? And could I substitute regular whole milk in place of coconut milk? Unfortunately these two ingredients aren’t commonly available in Pakistan but I don’t want that to stop me from trying these out! Thank you! 

  15. I knew these would be good, but they far exceeded my expectations. These taste so much like  “regular” cupcakes, that there is no longer a reason for me to feel deprived. My husband is gluten and dairy intolerant, so this is a fantastic treat.

    I did make a few modifications due to necessity. First, for the cake ingredients, I only had brown coconut sugar, and used 3/4c instead of 1c. The cake turned out sweet enough for our tastes. Second, for the frosting, I only had 2c of powdered sugar, so I cut the recipe in half, which made plenty for us. I did not have palm shortening, so I used goat butter, to see if my husband could tolerate it. So far he has not had any problems, but we will see after a few more days of these for dessert.

    One last thing, our storage in the fridge is pretty limited and I don’t have anything large/tall enough for 14 frosted cupcakes. I put the cakes and frosting in separate air tight containers and will frost as I go .5 stars

    1. So glad to hear that these cupcakes turned out great even with your slight modifications! Now you and your husband can have a treat where you don’t have to sacrifice flavor.

    1. Hi Connie- Yes! You can freeze either with or without the frosting. Both ways will hold up well, unless you want your frosting to be just a smidge more fluffier. Then save it for the day of.

      1. Do I need to put them in an air tight container or just any containers before I freeze them? Thanks

      2. Hi Connie – It’s probably best to put them in any container that seals well :)

  16. Can I substitute something else for the eggs? I have many options but didn’t know if it would work 

    1. Hi Danielle- I haven’t tried this recipe using any egg replacers yet, but you might be able to use a flax egg or mashed banana.

  17. Hi Lisa, I’ve made your chocolate cake recipe several times and am really looking forward to making these cupcakes. Can I substitute the palm shortening for vegan margarine? 

  18. Absolutely delicious!! My whole family loved them! The only thing I did different was to use golden monk fruit in place of coconut sugar. Thank you!5 stars

  19. Hi Lisa,
    I’ve made these beauty’s today. Just delicious thank you so so much. I thought I had coconut oil but I didn’t so replaced with vegetable oil. Still taste amazing. Will be making again and hopefully with coconut oil. My husband said they are so light and fluffy. A huge hit. Also my tinned coconut milk was heavy so I just whizzed it up in my vita-mix-perfect. Must go, chocolate cupcake and tea calling😋5 stars

    1. Hi Mary- So glad this recipe came together even with vegetable oil! Looks like you’ll have a winning chocolate cupcake recipe to whip up from now on :)

  20. Hi Lisa,

    I want to make these cupcakes, watched your video but I’m still unsure.  Can I clarify, is this coconut milk out of a carton or out of a tin?  Thanks Mary

      1. Thank you, I’ll be making them tomorrow. Stay safe and well and as always thank you xx

  21. Hi Lisa,

    Love your blog! It’s my first stop when I look for new recipes to prepare. I have been making your chocolate cake for every celebration in my house for the past 3 years! It’s a family favorite.

    I was excited to try out this recipe with my daughter for the new mini cupcake maker I bought her. I always use the metric measure for this cake and so we did the same with this recipe. As we were making the batter I realized the measurements were for the original chocolate cake! So once the first round of cupcakes were done, my daughter, who is 6, jumped ship and I ended up turning my kitchen into a mini-cupcake factory! I think I ended up making 54 mini cupcakes! Luckily we love this recipe so much we didn’t mind much, but just wanted to let you know so you can update the measurements. Btw, it works great with the electric mini cupcake maker. Also, I changed the plates in the machine and also made mini donuts! Which were awesome too.5 stars

    1. Hi Vanessa- Thrilled to hear that you and your daughter have enjoyed the chocolate cake so much! And I just took a look at the recipe card, and it looks like the measurements are correct! The ingredients are exactly the same as the chocolate cake, but I have adjusted it slightly. Just want to make sure you weren’t looking at the chocolate cake recipe by accident?

  22. YUM! Another winner in my house. You are making me look good LOL They were being eaten before the frosting was put on. And I thought frosting is the best part of a cupcake LOL Will make these again and again along with your Best Chocolate Chip Cookies that I make all the time. Thank you!5 stars

    1. Hi Christine – Amazing! Thrilled to hear you loved these cupcakes, along with the chocolate chip cookies :)

  23. Delicious!!! First time making paleo cupcakes; so easy, moist, and great chocolate flavor. Dangerous though, I want to eat them all.5 stars

  24. Just made this today for my husband’s birthday and made the recipe as written. The kitchen smelled so good while they were baking and they are very good! Husband approves! We are not gluten free but this recipe sounded so good I wanted to try it. It is moist and light and full of chocolate flavor.

    Just wondering what brand of full fat coconut milk you recommend? The one I used seemed hard to stir and get creamy.5 stars

    1. Hi Sharon- Happy to hear both of you enjoyed this even when you’re not gluten-free! And for coconut milk, I normally buy the brand Native Forest :)

    2. How long will these keep? I’d like to make a batch for my daughter’s classroom on. Saturday or Sunday, for consumption on Monday. Would they still be moist/fresh? Or do they need to be consumed same day?

      1. Hi Ingrid – you can find storage instructions on the post :) But you can either store in the fridge for up to 2 days, or freeze them for up to 2 months. If storing in the fridge, I suggest to make the frosting the day of and just give your cupcakes a little reheat in the microwave or leave them out at room temperature.

  25. Hi! 
    I would like to know if I can change the tapioca flour for more coconut flour? 
    And the vegan butter for ghee? 

    1. Hi Dana – no on the flour. Extra coconut flour will make the cupcakes really dense. But yes, you can substitute vegan butter for ghee.

  26. I tried the cake version and it came out great so I’m going to make these cupcakes for my work party. I was wondering if you’ve tried them with less sugar with any success? I know you mentioned using only coconut sugar to get those air pockets but I’m curious about using xylitol since they are also crystalline. Might have to try and let you know!  Also curious about not using eggs. Might have to try and see on that as well! Excited to experiment! 5 stars

    1. Hi Danielle – I haven’t tried these yet with less sugar, so I’m very curious to see how your experiment goes! Please do report back on how the turn out :)

  27. Hi Lisa, any suggestions on what I can use instead of  organic palm shortening? I’m not sure what it is. Can I use butter? Same quantity?

  28. These cup cakes are divine! Made them today, everyone loved them. I used only almond flour and coconut flour (its hard to find tapioca flour in Geneva- will widen my search next time) – and they turned out great. Thank you Lisa for sharing this wonderful recipe!5 stars

  29. Hi. I was reading the recipe and saw you use eggs. My daughter doesn’t eat eggs either. Would I be able to use nutritional yeast instead?
    Thank you for your reply. 

    1. Hi Adria – I’ll have a video on egg replacers soon! In the meantime, others have used a flax egg in this recipe with success. :)

  30. Bravo! 👏 Made these last night.  My kids are devouring them for breakfast!   I didn’t have tapioca flour so I used cassava flour instead and they turned out great. For the frosting I didn’t want to use sugar so I did just butter, cacao powder and 2 T maple syrup.  They turned out awesome.  5 stars

  31. These cupcakes looks so good and pretty!!!
    Can I use coffee extract instead of expresso powder? If so, how much?

  32. Hi Lisa, thanks so much for the recipe, the cupcakes look delicious!
    One question: Would normal milk or almond milk work instead of the coconut milk?

    1. Hi Luisa – You can use any other types of milk, however the consistency might not come out as creamy and moist – since the full-fat coconut milk is much more creamier.

  33. You read my mind!!! I made the chocolate cake a couple weeks ago and it was a huge hit for my big family! I was going to turn that recipe into cupcakes this weekend for my daughters birthday party. Thanks for posting this just in time! My mouth is watering just thinking about them 5 stars

    1. Hi Naomi – Wow, what perfect timing! Now you can make this recipe correctly for cupcakes :) Hope everyone at your daughter’s birthday loves these chocolate treats.

    1. Hi Debra – I haven’t tried this recipe with any egg substitutions yet, but I will be creating a video for egg substitutions very soon – so stay tuned :)

  34. Lisa, please describe and/or link the cupcake capacity you used for this recipe.  I’m not sure what size tin or cupcake papers to use or buy.  Thanks.

    1. Hi Terri – I’m always searching for ways to make paleo desserts delicious! And this one is definitely a winner :)

    1. Hi Erika – They sure are! If you haven’t tried my paleo chocolate cake yet, then this is a good start :)