Gluten-free Chocolate Cupcakes with Fudge Frosting
Requested at almost every family birthday party, these gluten-free chocolate cupcakes are topped with an amazing fudge frosting! This might just become your go-to gluten-free birthday cupcake recipe too!

After my diagnosis with celiac disease several years ago, one of the first desserts that I knew I was going to have to make gluten-free was chocolate cupcakes. I adore cookies and brownies, but if I HAD to pick my favorite dessert, it would be these gluten-free chocolate cupcakes with fudgy frosting. They’re my favorite gluten-free cupcakes!
This is the only thing I bake that I have zero self-control around. I will usually eat 3 of these gluten-free chocolate cupcakes per day until they are gone, which is definitely not good for the waistline! It’s definitely best if I make them when I have somewhere to bring them!
I’ve been sharing these super chocolaty, moist cupcakes with their fudgy frosting with people for years. They always receive rave reviews from everyone that tries them, whether they eat gluten-free usually or not. No one can tell that they are gluten-free!

These gluten-free cupcakes have the best texture on the day AFTER baking them, which I think is a big plus! I can whip these up the day before a birthday party, holiday get-together, or BBQ and save myself the work on the day of the event. Sometimes I’ll frost these the first day, sometimes I’ll wait to frost them until a few hours before I need them. You can store these at room temperature if your house isn’t overly warm, or keep chilled until an hour before serving.
This versatile recipe comes from my favorite recipe for gluten-free Texas Sheet Cake. If you’re looking for a potluck friendly dessert, go check that one out!

Notes on ingredients for gluten-free chocolate cupcakes:
- Flour: As always, I recommend using a good quality gluten-free flour blend that isn’t made of bean flours. I have had great success with the texture of these cupcakes when I use Gluten free Mama’s Almond Blend or Gluten free Mama’s Coconut Blend, King Arthur Measure for Measure Flour, and also with Cup4Cup flour.
- Baking cocoa: In this recipe, I like to divide the total amount called for and use about 1/2 of dutch-processed, Hershey’s regular or Saco blend cocoa and 1/2 Hershey’s special dark cocoa. That is how I achieve a deep, dark brown to my cupcakes and icing.
Here’s a look at how full to fill the cupcake liners before baking and what the cupcakes look like after baking. You’ll notice the cupcakes are mostly flat, making them perfect for frosting!

This frosting – you MUST make this fudge frosting! You will totally want to just eat the frosting with a spoon. My hubby and I will fight over who gets to lick the beaters when I make it. Thanks to my friend Steph for sharing this frosting recipe with me back in my college days!
No matter what new cake recipe I try out, I always use this frosting as it is simply the best chocolate fudge frosting there is!

Now I often do the frosting like I do the cake – with half regular cocoa and half dark cocoa. This pic shows you what the frosting looks like made with all regular cocoa (the lighter colored frosting) or with the blend with dark cocoa and regular together (the darker colored frosting). It’s completely delicious either way, or to make it fun, make a batch of each like I did here if you want the pretty assortment to offer.

If you use this frosting while still warm, it is easily spreadable and has a glossy finish when dried like you see in the photo of my gluten-free Chocolate Love Cakes but can slide off of whatever you are frosting. If you let the frosting cool completely before using, then it firms up and can be placed into a pastry bag for piping for decorating cupcakes like I did in these photos.
The chocolate fudge frosting can also be refrigerated to use later; just microwave 10 seconds at a time, and stir, until you get to the right consistency for piping or spreading. If you like a lot of frosting on each cupcake (or if you eat too much of it with a spoon!), then you might need to make another batch of the frosting to have enough. If you have any frosting left over, I put it in a freezer bag and put in the freezer to pull out the next time I need some extra frosting (or need a pure chocolate fudge fix!) For piping the icing on these to make a fun swirl, I used a tip from this Ateco Decorating Set on Amazon.
You can also switch up your cupcake liners and add sprinkles to make these work for whatever holiday or party you’re bringing them to. Here I used red/white/blue liners and sprinkles to make gluten-free patriotic cupcakes for a Fourth of July potluck:

For gluten-free Halloween treats, I simply found some Halloween cupcake toppers and used them, along with some Halloween cupcake liners. I usually find these Halloween cupcake toppers at Hobby Lobby – but other stores like Michael’s and cake/party decor places should have them too. I took these easy Halloween cupcakes to a Harvest Party our church was having. The gluten-free kids in attendance were so excited to have gluten-free Halloween cupcakes to win in the cake walk game.

My personal favorite way to enjoy the best gluten-free chocolate cupcakes is to pull them out of the refrigerator and put in the microwave for 12 seconds. With a glass of cold milk as a chaser, I am in heaven as I enjoy chocolate overload! I hope you can make this soon and enjoy chocolate overload with me!
Looking for some other yummy chocolate recipes? Try my flourless chocolate cookie recipe for a real chocolate fix. Next try this skinny flourless dark chocolate cake recipe – it looks so decadent!
Recipe for Gluten-free Chocolate Cupcakes with Chocolate Fudge Frosting:
Gluten-free Chocolate Cupcakes with Fudge Frosting
These super chocolaty gluten-free cupcakes are even better made the day before eating, making them a great choice for birthdays.
Ingredients
Cupcakes:
- 2 cups good quality gluten-free flour blend
- 1 tsp. xanthan gum *see note
- 2 cups sugar
- 1 tsp. baking soda
- ¼ tsp. salt
- 1 cup salted butter (2 sticks, 16 Tbsp.)
- â…“ cup cocoa powder *see note
- 1 cup water
- ½ c. buttermilk
- 2 eggs
- 1 tsp. pure vanilla extract
Fudge Frosting:
- ½ cup salted butter (1 stick)
- ½ cup cocoa powder *see note
- 3 â…” cup powdered sugar
- 6-7 Tbsp. milk
- 1 tsp. pure vanilla extract
Instructions
Cupcakes
- Line a muffin pan with paper liners and set aside.
- In your mixing bowl, combine gluten-free flour, xanthan gum, sugar, baking soda, and salt and set aside.
- In a medium saucepan, combine butter, cocoa, and 1 cup water. Bring just to boiling, whisking constantly. Remove from heat and add to dry ingredients, beat until combined.
- Add buttermilk, eggs, and vanilla and beat for one minute on low-medium speed.
- Pour batter into cupcake liners. I use a large scoop that measures about 1/3 cup batter into each opening.
- Bake at 350° for 17 minutes or until a toothpick comes out clean or with a few crumbs (no wet batter).
- Let cool in pan for 4 minutes, then remove cupcakes. Wait to frost until completely cool.
Fudge Frosting:
- Using a medium glass bowl, melt the stick of butter in microwave. Whisk in cocoa powder, then heat for 1 minute. Add powdered sugar and milk alternately, beating with a hand mixer until creamy. Add vanilla last, beating in until mixed well.
- If you use this frosting while still warm, it is easily spreadable and has the glossy finish when dried like you see in the photo but can slide off of whatever you are frosting. If you let it cool completely, then it firms up and can be placed into a pastry bag for piping for decorating cakes or cupcakes. The icing can be refrigerated to use later; just microwave 10 seconds at a time, and stir, until you get to the right consistency for piping or spreading.
Notes
*If your flour blend already contains xanthan gum or guar gum, omit the xanthan gum called for in this recipe.
As always, be sure to double-check your ingredients for gluten.
For the cocoa powder, I like to use about 1/2 of dutch-processed or Saco blend cocoa and 1/2 Hershey's special dark cocoa. That is how I achieve a nice dark brown to my cupcakes and icing.
*You can also bake this as a cake in a 9x13" pan for ~35 minutes or in two 8" cake pans for 22 minutes. Make sure to spray the pans well with non-stick cooking spray.

Pin these to your gluten-free desserts board here!

I hope you and your family enjoy these and think they’re the best gluten-free cupcakes like my family does!

The problem with this recipe is the so-called all purpose gluten free flour blend. Every brand of so-called all purpose flour blend is so different. Cup4Cup is mainly cornstarch. Bob’s Red Mill contains a lot of bean flours and sorghum. The results between these two flours will be vastly different.
There’s no such thing as all purpose gluten free flour. Failure to specify the gluten free flour blend in a recipe sets the baker up for failure. Gluten free flours are very expensive…both time and money tossed in the trash because the brand of flour used to develop the recipe was not specified.
I’ve learned the very expensive lesson to never use a recipe that does not specify the brand of all purpose gluten free flour used.
Unfortunately, these turned out terrible! They took much longer to bake than the recipe said, and then collapsed when I took them out of the oven. Also, they were not very chocolatey. I was very disappointed, as the recipe had looked delicious.
I usually never leave feedback for recipes but this one was fantastic. I made a batch for my patients for Christmas some allergic to gluten, the other to dairy. I used Bob’s Red Mills and had to make a few sibstitutions to accomodate them. As someone suggested, I added a teaspoon of baking powder. I substituted the amount of Xathan Gum for ground Flaxseed, half a cup of coconut oil and half of unsweetenes applesauce to replace the butter and lastly the buttermilk for 1/2 cup of Flaxseed milk witb a teaspoon of apple cider. I also cut thesugar to 1 1/2 cups. I was very nervous to change the recipe but they came out fabulous! The batter looked very thin a for a moment and freaked me out but they are delicious and airy. Thanks a lot for the recipe!
just got through making another batch of the icing. I do not think that you could mess this up. unless you burned the cho. I did not have a glass bowl so melted in a saucepan and it is still just as yummy. I think that maybe I did not add as much powdered sugar as the first time, but the taste is still very yummy. I am going to ice some more cupcakes and then use the rest of the icing to ice some brownies. Oh, my goodness. I can taste them now.
I just made these cupcakes and while they were baking they looked great. When I took them out of the oven, they sank in the middle. Can you tell me what I did wrong? I followed the recipe to a T. Thanks!
Hey Lisa, I read somewhere recently that it does not hurt to add a little more baking powder to a gluten-free recipe. I think I added a half teaspoon first time I made the cupcakes and they did not fall so you might try that. Also you do not say if you cook at high altitude or not, but that will affect it too. Good luck. They are worth perfecting.
I tried these cupcakes and icing and they are so good. I only made one change to the icing that I recall . It was because I had whipping cream I needed to use so used it instead of milk. It did not help thin the icing down any, but was it ever yummy and I ended up adding some evaporated milk to thin it down with so I pipe the icing on to the cupcakes. Also I use an oat based flour mixture as I can not have rice and I guess that makes two changes, but they are really yummy and I love the texture of them.
Sorry I forgot to rate. I would put a 4 1/2 on them.
At the beginning we didn’t melt the butter it was fine
And these are the best cupcakes I have ever had.
I made these cupcakes this week but replaced the water with brewed coffee and used a gluten-free flour mixture that included brown rice flour, white rice flour, tapioca flour, and potato starch. I also used a Bailey’s cream cheese frosting. They were amazing! No one even realized they were gluten free!
Delicious!! No one believed they were glutne free. I used bobs red mill 1 to 1 baking flour and they were perfect.
I topped them with Magnolia bakery vanilla buttercream recipe icing and they were heavenly.
Its a keeper.
Thank you!
Have you ever made these vegan, substituting applesauce for the eggs and a vegan apple cider milk mix for the butter milk?
I don’t know if it’s just that I’m a bad baker or what but they looked good at about halfway baking. At 17 minutes, they were spilled over and concave. I thought Bob’s Red Mill mix had xantham gum but it didn’t so I looked up substitutes and used gelatin. I also added 1/2 almond meal since Bob’s has a tangy taste to it (maybe from the sorghum flour?). THEN, as luck would have it, I was short on butter in total so I added some coconut oil. FINALLY, I cracked my second egg and it spilled on the counter but I used it anyway. The mix was fairly runny and still smelled tangy from the GF mix but wasn’t sure how to fix it by any means…suffice it to say, looks like store bought baked goods are the way for me! I used accurate measurements but a few substitutes. I guess that’s the difference between a cook and a baker. They don’t mix well in my brain!!!
Made these last night. I didn’t have bakers cocoa, so I used a few chunks of a dark chocolate (65% cocoa and with crystallized ginger) bar. These are absolutely delicious! Nice and moist! This will definitely be my go-to recipe for any cake / cupcakes in the future!
Hi Michelle, I made these over the weekend for a 60th birthday party. I was nervous because I hardly ever bake cupcakes from scratch, let alone gluten-free – and they were spectacular! Everyone loved them and asked for the recipe. I got 22 cupcakes from my mixture. I noticed that when I baked the second batch (I had to do it in two batches), it took longer and also seemed ‘watery’ after the 17 minutes were up (as someone else mentioned). But I simply left them in for longer and kept an eye on them, and they were perfect. I suspect it’s because that half of the batter sat for about half an hour before going into the oven. The icing (that’s what we call it in South Africa) was great too. Thanks for this fabulous recipe!
These are amazing!!! I made them for my daughters 2nd birthday last month! We couldn’t believe how good they were! I Made the Texas sheet cake version yesterday when family came to visit! What a hit =) thank you for another great recipe!!!
I have had Celiac for many years now. When I found out I was Celiac, I thought my cooking good creative meals and desserts was over. Now a job change has felt me to create in my kitchen again. I am trying your chocolate fudge icing tonight. It sounds good and easy enough. I can’t wait.
Can I use a flour blend of, brown rice,white rice, potato statch, tapioca flour , cornstarch and xan, gum? Do I need to add some almond flour to make your chocolate cupcakes? Thank you linda
You didn’t use any almond flour?thanks linda
Linda, this recipe is fantastic and I make them all the time with out any almond flour. My blend is similar to yours and it should be fine!
Hi,
Your cupcakes looked great so I tried to make them. I didn’t have buttmilk, so I substituted kefir. They flopped. How important is the buttermilk? Should the chocolate/butter mixture be thick after cooking?
Mary,
The butter/cocoa/water mixture will be quite liquid after cooking. You are just cooking and whisking to combine them well. If yours was thick, it could be a mistake,
I have not done any baking with kefir, so I’m unsure whether that is a suitable substitution for buttermilk. Hope you’ll try this again when you have the right ingredients. You’ll love them!
I made these cupcakes egg free and milk free. I used 1/2 TBSP white vinegar with enough soy milk to make 1/2 cup. I used flax seed to replace the eggs (1 TBSP flax seed and 3 TBSPs water for each egg) and added 1 Tsp baking powder. They are so good!!!
Oh, Michelle! These chocolate cupcakes are fabulous and just what I was looking for. Per your suggestion, I made them yesterday and frosted them today. Couldn’t wait to try one and they are seriously yummy…so moist and chocolatey. I gave them (well, MOST of them anyway) to my brother-in-law who has had to go gluten-free and he is a chocolate fanatic. He’s gonna love them. By the way, I used King Arthur’s Gluten-free Multi-purpose Flour and added 1-1/2 teaspoons of baking powder as “insurance” against sinking in the middle after baking and they came out beautifully. I’m gonna try your white cupcakes next. Thank you so much for sharing.
P.s. My brother-in-law just emailed me that he loved these cupcakes! Thanks again.
Kasha,
Yeah!! Thanks so much for letting me know! These are a favorite of mine! Glad your brother-in-law liked them too.
Hi, I was wondering if you could recommend a flour substitution… my son can’t have almond or coconut. I usually make my own flour blend using amaranth, teff, sorghum and oat flours and potato and arrowroot starches, but I think that might be too dense? (And we’re also cutting out oats, even GF oats). Also, do you think it would really change the cupcake if I used ground flax or chia instead of eggs (eggs are on his list too).
Kristy, If you’ve found your own mixture that seems to work for you in other baking recipes, feel free to try it here. The other all-purpose gluten-free flour blends that I recommend that don’t have almond or coconut flour in them are gfJules and King Arthur Flour. Hopefully those would fit with his allergies.
I haven’t tried these with the egg adjustment. You’ll probably just need to give it a shot and see how it goes. Let me know whether it works or not. Good luck to you!