These paleo chocolate cupcakes are moist but not eggy and have a rich, dark chocolaty taste! Topped off with chocolate fudge frosting. Grain-free, gluten-free, and dairy-free. Scroll down for a how-to recipe video.
So here’s the promised cupcake recipe that I used as a carrier for the paleo vegan chocolate frosting that I posted last week.
Before anyone gets their knickers* in a twist, I know sprinkles aren’t paleo. They’re, like, the very opposite of paleo. But just look how they brightened these cupcakes up! They look much happier with the sprinkles.
Here’s how you can make your own paleo coconut sprinkles. The recipe uses plant-based natural coloring and coconut and while they’re not nearly as bright as nasty store-bought sprinkles, you don’t have to worry about what you’re eating!
Raspberries, strawberries and mini chocolate chips would also make for pretty and delicious paleo alternatives to sprinkles.
* I don’t think I’m British – I just loathe the p-word.
This paleo chocolate cupcakes recipe is pretty much the same recipe I used in my spiderweb cupcakes. I adapted it a little to make the cupcakes bigger and to make the measurements a bit easier for people who use measuring cups instead of grams.

I also added a little more sweetener! The original paleo cupcake recipe was sweetened with just honey but when I tried the recipe as written, and ate a cupcake without the frosting, I wanted more sugar. So I added two tablespoons of coconut sugar.
These gluten-free dairy-free cupcakes have a really interesting texture and I don’t mean that in a bad way! It’s hard to describe, but they’re kind of mousse-like. They’re not like regular, fluffy airy cupcakes, but they’re moist and… mousse-like. I’m sure that won’t convince you to make them so here’s a review from the original recipe:
“A girl who has been eating GF for 3 years said they were the best GF cupcakes she has ever had! They were all asking after the recipe!” I think they’re pretty darned delicious but I don’t know about best gluten-free cupcakes ever. I think I’ll reserve that title for cupcakes that have the same exact texture as regular cupcakes. Ones where you have no idea that they’re gluten-free (like my best gluten-free brownies recipe!)
These paleo chocolate cupcakes don’t have that typical weird, eggy and spongy thing that a lot of grain-free cupcake recipes I’ve tried have had, though so that’s a huge plus. All in all, I’d say that these cupcakes are a victory. :) Check out the reviews in the comments in you need convincing!
For more of my most popular paleo recipes, try my chocolate chip paleo cookies or these paleo blueberry muffins! I can pretty much guarantee you that neither will disappoint. :)
I definitely need to up my paleo cupcakes game (when it comes to variety!). These chocolate cupcakes are pretty much all I have. What kind should I make next?!
Paleo Chocolate Cupcakes (grain-free, gluten-free, dairy-free)

- Prep Time:
- Cook Time:
- Ready in:
- Yield: 14 cupcakes
Ingredients
- 3/4 cup + 2 1/2 tablespoons (104 grams) Dutch-process cocoa powder
- 2/3 cup + 2 tablespoons (80 grams) almond flour or almond meal
- 1 1/2 teaspoons baking powder (use paleo baking powder, if necessary)
- 1 teaspoon espresso powder
- 1/4 teaspoon salt
- 1/2 cup + 1 tablespoon (126 grams) coconut oil, melted
- 2/3 cup (213 grams) honey
- 1/2 cup + 2 tablespoons (160 grams) unsweetened applesauce
- 2 tablespoons coconut sugar
- 4 large eggs, room temperature
- 1 tablespoon vanilla extract
- for frosting: 1 or 1 1/2 batch paleo chocolate fudge frosting1
- paleo decoration ideas: raspberries, strawberries, mini chocolate chips, homemade coconut sprinkles
Directions
- Preheat your oven to 350 °F (175 °C) and line a muffin pan (or two) with 14 liners.
- In a medium mixing bowl, stir together the cocoa powder, almond flour, baking powder, espresso powder and salt. Set aside.
- In a large mixing bowl, stir together the melted coconut oil, honey, applesauce, coconut sugar, eggs and vanilla. Add the dry mixture to the wet and stir just until combined.
- Pour the batter evenly into the muffin liners, about 3/4 full.
- Bake for 24-28 minutes. A toothpick inserted in the middle should come out mostly clean. A few moist crumbs or a little stickiness is okay, just not raw batter. These are super moist so if it comes out totally clean, they're probably overdone.
- Let cool for 5 minutes and then remove to a wire rack to cool completely. These do not taste very good straight out of the oven. I recommend letting them sit for 2 hours and then frosting. When you refrigerate them, they become denser, the way brownies get when you refrigerate them. Can be kept at room temperature, unfrosted, for up to 3 days or can be refrigerated for up to 5 days.
Notes
- 1 batch of frosting will yield just enough for slightly more than 1 tablespoon of frosting per cupcake, which isn't very much for frosting lovers. You may want to do 1 1/2 batches or even a double batch if you want to frost the cupcakes more generously. I used about 1 1/2 tablespoons (1 1/2 batches) of frosting on mine.
224 comments on “Paleo Chocolate Cupcakes (gluten-free, grain-free, dairy-free)” — Add one!
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What a pity! Did you make any changes at all to the recipe, like maybe using Hershey’s instead of Dutch-process cocoa powder? I ask because all the other reviewers who followed this recipe (most of them are on the first page of comments when you click “Older Comments”) seemed to have loved them!
According to this and this page – cacao powder is more bitter than Dutch-process cocoa powder. So that could be your problem since you found them bitter and nobody else has mentioned these having a bitter taste. “Dutch-processed cocoa powder (dark cocoa) is cocoa powder that has been processed with an alkalized solution, making it less acidic and much richer in taste. Regular cocoa powder retains a more acidic nature and bitter taste.”
Unfortunately not. Since this recipe makes 14 and you’re wanting 12, you’d have to multiply every ingredient by .85, which is not a nice number to be messing with when it comes to fractions and baking.
So, I was reeeaaallly skeptical about these and as they baked, they did not smell like traditional cupcakes. But after they cooled and were frosted, they were excellent. Truly delicious! I did add 1 Tbs. of powdered sugar to the frosting for a little sweetness. So pleasantly surprised – I’ll be making them more often! Thank you!
I’m so sorry I somehow missed your comment! I’m so happy that you enjoyed the cupcakes and that you’ll be making them again. :) Thanks a ton for your feedback!
What could I substitute for the Almond Flour? We have a nut and grain allergy in my daughter’s class, but I want the little boy to be able to have a cupcake when I bring some in for her birthday next week.
Thank you!
Unfortunately, nuts flours aren’t interchangeable with non-nut flours. I’ve heard of people using sunflower seed flour as a sub but I’ve never tried it and have no idea if it’d work here. Sorry about that!
Hi Sarah,
I’ve had great success subbing tigernut flour for almond flour in many of recipes with a 1:1 ratio. I plan to try this with cacao and tigernut flour.
Thanks for the tip! I’d love to hear how it comes out with your sub.
I love how the frosting looks so fresh and moist.
Haha. Thank you! I like that, too. ;)
Hi -could this be made into a cake?
Hi! A few commenters have so you may want to look there. I also made it into a paleo chocolate strawberry cake using 6″ pans. Hope you’ll enjoy it!
I have been finding many Paleo or Glute-free recipes but no nutritional values are attached. I really need to know total calories, sugar and salt, etc. Do you have that information for your recipes?
I don’t have that info but you can copy and paste the recipe here for the nutritional profile, if you’d like. :)
The expresso powder, is it necessary?
It just brings out the chocolate taste.
Hi, I was wondering if the coconut flavor of the oil comes through in the final product.
I’m trying to piece together a [refined] sugar-free German chocolate cake for someone at work and I think this recipe is a winner for the cake portion :D
Hi there! You can’t taste it at all if you use refined coconut oil. I haven’t tried this recipe with unrefined coconut oil so I can’t say for sure, but I’m guessing there might be a slight coconut taste then. I hope you’ll enjoy them!
I just made this and wow! Super fudgy, therefore do NOT bake in a bundt pan…it won’t come out xD
Needless to say, I immediately made a second batch – this time as 2 9″ rounds. The only thing I altered was using about 25g of agave to complete the honey (I ran out).
From what I can taste in the failed bundt, this cake is insanely moist and fudge-like! It really is amazing. It tastes like fine dark chocolate cake. This is soooo a keeper!
Aww. I’m sorry the bundt didn’t come out well! I have had the worst time converting grain-free recipes to bundt pans. They almost never work for me! I’m happy the 9″ rounds worked out well. :) Did you double the recipe for that? Or were the layers very thin? I’m so very happy that you enjoyed the cake! Thanks a bunch for your tips.
I´ll try these tomorrow! They look so yummy, thank you! Can I replace honey with raw sugar? Do you have any idea of the equivalence? Thanks!
That’d unfortunately throw off the liquid / dry proportions so I wouldn’t recommend it. Maple syrup or another liquid sweetener should work! I hope you’ll enjoy them. :)
Getting ready to try these! I need a sugar-free not necessarily paleo. Can you use a substitute for the coconut sugar like Splenda? Thanks! Debbie
I’ve never used Splenda (or any sugar-free sub) so I really don’t know. Sorry I’m not more of a help!
I made these for my birthday yesterday, and they were incredible! I shared them with family members who don’t eat gluten free, and they went back for seconds. Thank you for the wonderful recipe that I will continue to make over and over!
That’s always so nice to hear that non-GF eaters went back for seconds. :) Thanks a bunch for your comment! I hope you had a great birthday.
These were amazing – left out apple sauce as I didn’t have any. Also left out coconut sugar. They were like mini mud cakes – I added a little sea salt to the top and left off the frosting. Will definitely be using the recipe as my base for paleo cakes. Best cake recipe I’ve come across – thanks
That’s amazing that they came out well without the applesauce and coconut sugar! That’s quite a bit less sugar. :) I looked up mud cakes and am not really sure what they are. Does mud cake have a gooey texture? Most of the ones I looked at just looked like regular cake. I’m interested in trying your version, which is why I ask. :) Thanks a bunch for your comment!
They were dense – but soft – if that makes any sense. I kept them in the fridge. I just loved them. Might go make some now. 😊 I’m now interested to put the apple sauce and sugar in so I can see the difference 😊
It does make sense! And I bet you will notice a difference. It’s quite a bit of sugar. ;)
These cupcakes look perfectly moist and delicious. However I would love to make these nuts free so I can take to my kids school to share with friends and here in Australia, schools have a nut free policy. Is there a suggestion you could offer as a substitute for Almond flour/meal?
Thanks! Unfortunately, nuts flours aren’t interchangeable with non-nut flours. I’ve heard of people using sunflower seed flour as a sub but I’ve never tried it and have no idea if it’d work here. Sorry about that!
Hi there!
I am trying to do a no sugar version. Is there any substitute I can use for the applesauce that you know of? Thanks!
Hello! Unfortunately not. You could try another type of fruit (not that I’m sure that’d work) but that doesn’t help with the sugar problem. Sorry about that!
I left out the apple sauce when I made them as I didn’t have any – they were the most devine paleo cupcakes I have baked. Like mini muds – I did make mine in mini cases not sure if that would have changed anything. I’d encourage you to give them a go without the apple sauce 😊
Is there anyway I can get away with leaving the expresso out? Will it still come out ok?
Just leave it out and they’ll be totally fine. :) Enjoy!
These are FABULOUS! The only changes I made were: used 1/2 C of Raw Honey and I used Hershey’s Dark Chocolate Cocoa Powder and Trader Joe’s Instant Coffee Powder instead of the Espresso Powder. These are so great. Thank you for the recipe! I’ll be making these often!
I’m happy that they came out well with your changes! Thanks for sharing. :) I’m happy to hear that you’ll be making them again! Thanks a bunch for your feedback.
Thank you for this recipe! Made it for my office and they LOVED it. And this is not a paleo crowed, so way to go!
I ended up having plenty of icing leftover with just a single batch.
That’s great that you and your co-workers enjoyed the cupcakes! That can sometimes be tough when you bring paleo goodies. ;) Thanks for your feedback!
Made these for my husband’s birthday and everyone loved them! They taste amazing cold! Thanks so much for the recipe!
I also used about half the honey and they were plenty sweet enough!
Awesome! Good to know. Thanks. :)
Yay! So happy that everyone liked them. :) I hope your husband had a happy birthday! Thanks for your comment.
Hi! These look so great! Can I use coconut flour instead of the almond flour?
Hi there! Coconut flour is unfortunately not interchangeable with any other flour as it absorbs so much more liquid. Sorry about that!
Just made them with coconut flour before I read this and they turned out fine. I used a little bit less than the almond flour and they’re probably a bit drier, but still super tasty.
Great recipe! And I’m not gluten-free or dairy-free usually. Yum 👅
Interesting! I’m happy they came out well. They’re supposed to be super moist so I hope you get to try them with the almond flour some time. And I’ll try with coconut because I’m interested in how they come out! Thanks for your comment. :)