Gluten-Free Chocolate Brownie Cupcakes with Chocolate Ganache Frosting

Ali Segersten Apr 09, 2009 68 comments

You are in for a real treat today! The other night I had an early morning dream of these cupcakes with the recipe clearly spelled out for me. I was in sort of a lucid dream-like state and knew I needed to write it down. But alas, I have been exhausted caring for my children who have the chicken pox (and Tom who apparently did not have them as a child). So I fell back asleep with them playing on the bed. The next time I awoke I had the recipe in the forefront of my now awake mind. I asked my seven year old, Lily, to run and get me a pen and paper. I quickly wrote it down before it disappeared into my daily routine.

I don't know if it was because I was reading Shirley's GFE blog the other night and looking at her delectable chocolate cake or what - but this type of recipe is not the norm for me. I have never made anything completely from almond flour and vegan nonetheless!

But here it was, so I thought I should at least try it out. Since the only almond flour I had was Bob's Red Mill (a rather coarse blanched almond flour) this is what I used. The result was very tasty and brownie-like but too chunky. I knew there were finer ground almond flours out there, so I googled it. Lucy's Kitchen Shop popped up. I had heard of Lucy before because she is local and has written a Specific Carbohydrate Diet cookbook that was displayed next to our cookbook at our local Co-op when it first came out.

Naturally, I called her up to see how soon I could get some of this very finely ground flour. She was lovely to speak with and I paid over the phone and stopped by her house a few hours later to pick it up!

Today I tried them with my new flour and they are oh so delicious! Simple ingredients but the end result is rich and delicious with a full-bodied chocolate flavor. This cupcake is not for the faint at heart! I had planned on posting my Lemon Poppy Seed Tea Bread for Easter but since this recipe came to me I thought I would share this one.

Now, if you are willing, I would love to know what interests you the most as far as gluten-free baking goes. Vegan? Sugar-Free? Grain-Free? Nut-Free? Everything-Free? Just Gluten-Free? Your feedback will help me with the next book (hint, hint) I have been working on. I would love to hear from you! There is a "Comment" section you can click on at the bottom of each post where you can leave a little something for me to read. You can also email me but your note may get lost in the sea of emails I receive. (If I have not responded to an email you sent, I am very sorry, just busy, please send it again!)


About the Author

Ali Segersten

Alissa Segersten holds a Bachelor's of Science in Nutrition from Bastyr University and a Master’s of Science in Human Nutrition and Functional Medicine from the University of Western States. She is a Functional Nutritionist, the mother of five children, a whole foods cooking instructor, professional recipe developer, and cookbook author. She is passionate about helping others find a diet that will truly nourish them. Alissa is the author of two very popular gluten-free, whole foods cookbooks and guidebooks: The Whole Life Nutrition Cookbook and Nourishing Meals. She is also the co-author of The Elimination Diet book. Alissa is the founder and owner of Nourishing Meals®.

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for whomever posted this, you can use carob chips i would imagine. Available in most health food stores.

in case any one hasn't mentioned it already, if you have a high-powered blender like a vita-mix or a juiceman smoothie machine, you can buy the coarse flour (because it's easier to find) and grind it finer on the highest setting.

I'm looking to make these for my son's birthday this weekend... wondering if these (along with your other cakes and cupcakes) can be made ahead and frozen? Hoping so as they look delicious!!

thank you posting the recipe, I am grateful.
I had a difficult time with these, they looked great, and then sank. I wonder if overmixing them does that, or too much flour? I used honeyville flour, and followed the recipe as well. I did have a lot of batter, and filled them full. I wonder if I had filled them less, if they won't have sunk. Just wondering if any feedback.
Thank you again, I enjoy your site, and have had much success with other recipes.


I'm doing a full elimination diet. (no corn, gluten, soy, citrus, chocolate, coffee, tea, sugar, dairy or eggs.) I'm looking at the post for
"Vegan, Grain-Free, Sugar-Free Chocolate Brownie Cupcakes" and wondering what to substitute for Dagoba Chocodrops. I am subbing carob powder for cocoa but am unsure about the chocodrops. Thanks!

I'm brand new here, my naturopathic doctor sent me here to try one new recipe a week. I really love the looks of these recipes! I love baking, but my daughter has a kid in class with a tree nut allergy so all almond products are out. Is there somewhere to figure out a conversion of the different flours listed on this website? If I don't have one, but another how much do I use? Is it one for one?For example, what can I substite for the almond flour in this yummy looking recipe?

Just shared on my FB page :-). My readers love it!

Joyful Melody - Yes! You can make them without the xanthan gum, just add an extra 2 tablespoons of arrowroot in the dry ingredients (I don't think starches are GAPS friendly though) and use honey or coconut nectar to replace the agave, and melted coconut oil in place of the grapeseed oil. I modified this recipe a while back and put it into our new cookbook:

Enjoy! -Ali :)

would these work without the xanthan gum? It is corn-derived, so not technically grain free (but more importantly we have a corn allergy). Also we're on GAPS so we have to use you have an idea of what the measurement would be for honey?

posted on my Facebook for all my Whole food friends to see!

Yes Agave nectar is a well marketed sugar it is as strong on your pancreas-

It's a starch similar to corn syrup. On that note re sugar you might like this interview to help kick the habit!

I have yet to give it up completely myself...but this has inspired me to find your blog.

I like the look of your cupcakes, Im thinking on what to sub your syrup with maybe mashed banana except due to our disastrous rain storms last year bananas are at a premium and rising here in Australia. Maybe smidge Stevia with something moist...

You can easily make almond flour by grinding whole or slivered or flaked or blanched almonds in a coffee grinder. Grind it again to refine it. X

I should specify - I'm particularly interested in sugar-free baking that uses stevia, applesauce, etc., rather than agave or honey, which I use in very small quantities but try to avoid.

I am really interested in sugar-free baking - I'm on a (moderate) candida diet so the sugar-free recipes are fantastic for me! I've checked out other gluten-free blogs/cookbooks but a lot of them still use sugar, so I'm happily trolling through this site for the sugar-free recipes!

I am really interested in making this recipe but I'm wondering if you have a substitute for the Xantham Gum to make these truly grain-free. Thank you!

These cupcakes are fantastic! These are the first things that my 16 year old son has really loved since I started cooking gf. We decided to top these with your raspberry sauce. I used your blueberry sauce recipe and subbed raspberries. They were delicious. Thank you for your cookbook and your blog.


going to bake these today!! i love the natural sugar recipes that are gf and vegan.....i would love to have recipes in my dreams...means you are definitely doing something your are passionate about! thank you for the blog, can't wait for the cookbook!

WOW! These cupcakes are amazing! I ordered Lucy's almond flour as you suggested and was so happy with these. I'm grain-free, egg-free, dairy-free etc right now, and these deliciously moist cupcakes were exactly what I've been hoping for! THANK YOU! :)

Made these last week as a treat for the husband and I finished them in three days! So fantastically rich! I used Bob's Red Mill almond meal since that was all I had on hand, and they have definite texture, but I think that adds to the "brownie" experience.

I WILL make these again, and hopefully won't snack too much on the batter next time :)

I'm always looking for gluten free and sugar free baking ideas! I can only tolerate 1 tsp of honey or agave at one time, so I have to reduce the amounts of sweetener in your recipe. How about a book with more recipes like that? I do use stevia a lot, but I don't like it much in far.

I am very interested in gluten and sugar free. Recent studies have shown that agave nectar is equally as bad as sugar, so regretably, I don't consider these sugar free.

These still taste great after freezing (and reheating in the microwave) but are pretty crumbly...any suggestions for making subsequent batches? I was thinking of adding an additional 1/8 tsp of xanthan gum or possibly an egg...Thanks!

These chocolate brownie cupcakes are DELICIOUS! So moist and sweet - but not too sweet! I love that they are relatively low glycemic, composed of whole foods, easy/quick to prepare (and bake!), and FUDGY! My husband really likes them too! We didn't frost our brownies since they are sweet enough and we plan on freezing some for a quick breakfast or snack after our baby girl arrives! Thanks for the great recipe!

This recipe sounds great. I can't wait to try it. For the cookbook I would love to see Vegan and Sugar free recipes.

re: Gluten-free Chocolate Brownie Cupcakes. I made this recipe this afternoon. I have tried many, many recipes that don't contain flour, eggs, sugar or butter and NONE turned out nearly as good as this one! THank you so much for creating it. The cupcakes are delicious, moist and hold together perfectly. My husband who turns his nose up at my usual creations ate one and pronounced it delicious.
I altered it a bit, using only 1 teaspoon of baking soda and honey instead of agave nectar, and I had to cook it 5 minutes longer and I didn't make the icing - it doesn't need it.
Here's a question for you: have you seen a cookbook for fermented foods? I'm experimenting with various liquids in place of milk - the latest was corn milk I blended up, but it's not that great.

Thanks so much for this recipe. I have been searching the web for a cupcake recipe that uses almond flour and frosting that uses agave! I make my own almond milk and love using the meal that is left over for gluten free breads and deserts. I found that if you dehydrate the almond meal that is left over from the almond milk process, it works great in baking.
I will definitely be making these today.

I really appreciate attempts at grain-free / sugar-free baking, but it worries me that so many people seem to accept agave as a healthy substitute for sugar. Agave is just another concentrated sweetener and is actually higher in fructose than high-fructose corn syrup! Consumption of concentrated fructose has been proven to be a huge contributor to metabolic syndrome, and thus diabetes and heart disease.

I know some people have a hard time with the idea of giving up sweeteners altogether and everyone ultimately has to make their own decisions regarding what's right for them and their fmaily. But please don't fool yourself into thinking that agave is a health food or is somehow not sugar.

I am very interested in GF, vegan, and sugar free baking. My partner has sensitivities to all of these things, but I love baking. I've been using Cybele Pascal's cook books which I like. And, I've also been venturing into converted my own recipes. I'm having a ball and so glad to find your web site. I've also got your cook book and looking forward to the next one.

These cupcakes are spectacular. My favorite GF recipe so far...and vegan to boot! As for the nut free thing (I didn't read all the comments to see if it was addressed) I also tried it with a combination of GF flours such as Sourghum, Brown Rice and Buckwheat. Also, if out of Arrowroot, corn starch worked as a great alternative. YUM!

Thanks so much for this fabulous recipe.


My vote would be for gluten free and vegan. As we're not dealing only gluten allergies but also dairy & egg allergies. I just discovered your blog and I'm really looking forward to trying your 'dream cupcakes'.

I've got these in the oven now and they look awesome. The batter was delicious. I ground my own almonds and didn't quite have 2.5 cups, so added .5 cups of millet flour. And I don't have grapeseed oil, but did have macadamia nut oil, so subbed this. The batter tastes like chocolate and peanut butter. Yummm....

Thank you! I love grain-free baking!

Looks good. I'm thinking about trying it. I'm trying to be meat-free and grain free and sugar free but not vegan. Anybody have any books or sites to recommend?

I made these cupcakes earlier today and they were a big hit! So delicious! They were rich and sweet. The coconut milk and almonds makes them moist and creamy.Honestly you don't miss the grains at all.
I must admit that the almond flour is a little pricey where I live in Hawaii, 3 cups was $12.99 at my local health food store.
Regardless, I absolutely recommend these to everyone!
Thank you so much for this recipe.

Thanks for your comments, Susan - Lucy's Kitchen Shop sells the perfect type of blanched almond flour for this recipe - the link is in the post. The strained off almond pulp sounds like a creative way to use it up - I might try that sometime, thanks. :)

Val - I followed the Body Ecology Diet about 10 years ago with great results, none of my symptoms returned after going off the diet. I would recommend this book. The only allowable grains are millet, amaranth, and quinoa. Quinoa for breakfast is yummy. You can make a topping by cooking fresh (or frozen) cranberries in a skillet with cinnamon and stevia with a little water to create a sauce for the quinoa. For desserts using xylitol/stevia I would recommend going to Lauren's Healthy Indulgences blog - it is gluten free/sugar-free. She uses xylitol to sweeten. Also check out Kelly's Spunky Coconut Blog (and her cookbook). Both links are in the sidebar under "Other Gluten-Free Blogs" - hope this helps! -Ali :)

Hi Ali, having recently started on the candida diet, I'm interested in sugar/wheat/gluten free recipes (most recipes I find have at least one of these ingredients). It's so hard to find tasty ones. Yours seem very appealing, although I'm not sure if agave can be replaced by the allowable diet sweeteners (stevia/xylithol), without suffering on the taste. Any suggestions? Breakfast/dessert recipes would be great. Thank you!

The recipe is great! I agree with the comments on the almond flour being on the coarse side. I make my own almond milk, and I find that the almond meal I strain away from the milk is about the perfect consistency for this recipe. Its also a lot less expensive and far easier to come by.

I was looking for something creative like this. Then tried this awesome recipe. This recipe does not disappoint. It's a snap to prepare and really tasty & healthy.

Ali - thanks so much for your generosity in sending me home with a few of these lovely muffins. I couldn't believe they were gluten and dairy free! My daughter, husband, and I absolutely loved them!
Thanks again!

These cupcakes are divine Ali! I am so happy you had this dream. We have made them twice already and they are perfect each time. I have shared them with friends and told them about your blog. I keep meaning to leave a comment but have not had a chance until now, hope its not too late.

I am most interested in egg-free, gluten-free baking using whole food ingredients.

Thanks again! Lillian B.

i am so glad that i found your blog today. i am nursing a wheat-dairy-nut-allergic child, so i am naturally eating the same way.

Thanks for all of the comments everyone, I very much appreciate your feedback! I will let you know more about the book in the coming months.

Helen - yes - do not chill the frosting or the cupcakes w/frosting because it will become very hard.

When you say do not chill, do you mean don't chill the whole cupcakes or just the frosting before you put it on the cupcakes (as it would go solid and therefore not spread?).



You and Shirley are going to get me baking yet. You keep tempting me with these delicious looking chocolate treats that have all the ingredients I can eat. I know if I bake them I won't be able to control myself so I'll need to have a party and invite everyone over to give them a try. Now I just need to order some almond flour. It keeps popping up in different blogs I'm reading. Elana's Pantry has written a whole cookbook on it. I still don't know how you have time for all of this. Hope everyone is finally healthy!

I forgot egg free too!!

Hey Ali!
Holy bamoly!! These look SUPER yum.
Now if only those Dagoba Chocodrops did not have cane sugar in them. I wrote to them about this, but they said the market for an alternative sweetened chocolate chip was not large enough. Dang!
As for what I like in a cookbook- dairy, gluten, soy, and cane sugar free are the main ones. I also cannot have white potato. I LOVE chocolate. So, dairy sugar gluten free chocolate recipes (like this cupcake!!) would be fantastic :-D
Main course meals free of all those things are always appreciated too since I get stuck in a rut with the same old stuff all the time.
You are great, thanks for this recipe!! <3

Hello, Ali, from Arkansas... You have your hands full with the pox, it sounds like. I wish all the kiddos and esp. Tom a speedy recovery... You need him!! We love almond meal - I often throw a bit into pancakes or whatever I'm baking. I'm most interested in egg-free since that is our known allergy. But also, I really appreciate your use of a variety of nutritious grains and other ingredients, just to add more vitamins and minerals and diversity to our diets. Also, sweet-tasting, but sugar-free/low glycemic works well for us. Those cupcakes look tasty!! xo - April

These look sensational and I can't wait to try them! I'm intrigued by them being vegan, grain free, sugar free and chocolate! Thanks!


I will definitely be purchasing your new cookbook when it comes out! I would love to see a few recipes in your book that are gluten-free, dairy-free, sugar-free, and soy-free all within the same recipe. These are hard to find. Looking forward to your new book!

And soy free! I am making these tomorrow to take over to a new special someone's house.

Personally I'd like to see some hypoallergenic recipes that would also be appropriate for someone recovering from adrenal fatigue. I'm also curious to learn some new ways to use millet and wild rice.

I am so excited to hear of a new cookbook from you! I picked up the other one last year at the (Bellingham) Co-op. Newly gluten-free, I am looking forward to taking a cooking class from you as well.
I would love to see many lactose/dairy free recipes included too, and maybe some recipes using Stevia as the only sweetener. I would LOVE to see some other recipes, or ideas, for candida as well - no mushrooms, vinegars, etc.
Looking forward to your book. Good luck with the spotty family. :)

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