Paleo Chocolate Fudge Cupcakes {Dairy-Free, Gluten-Free, Grain-Free, No Refined Sugar}

Prep 10 minutes
Cook 20 minutes
Servings 12

Grain-free never tasted better! My easy and super moist Paleo chocolate fudge cupcakes will satisfy your chocolate cake cravings. Made with simple and healthy ingredients. Gluten-free, dairy-free, grain-free and no refined sugar. Yes, even the glorious chocolate fudge frosting!

Three Paleo chocolate cupcakes with chocolate chips and a glass of milk

Paleo Chocolate Cupcakes

Yesterday was my husband’s birthday, and I wanted to bake him something special.

He is trying to stay away from grains and dairy because of migraines and autoimmune inflammation, so I needed to find a Paleo cupcake recipe.

After doing a search for Paleo cupcakes on Pinterest and not quite finding what I was looking for, I decided that I would try to make my favorite cupcake recipe grain-free.

I have something to admit friends, that grain-free baking is a whole new world for me. I was a little nervous about stretching outside of my normal gluten-free baking comfort zone, but these fudgy beauties turned out awesome!

Grain-Free Baking

Most gluten-free flours that I use are made with rice flour. Rice flour mimics the taste and light texture that a wheat flour would produce. Grain-free flours, like coconut and almond flour, do not have the same texture or flavor. They produce a denser, heavier cake.

Also, you can taste the light nutty flavor of the coconut and almond flour. So here is my disclaimer friend, if you have never had grain-free cake or cookies, it will be a lot different in texture and flavor than what you are used to. It is not a bad different, but your cakes and cookies will be heavier and denser.

overhead shot of three Paleo Chocolate Fudge Cupcakes with chocolate chips and a glass of milk

Dairy-Free and Refined-Sugar Free

Now that I have given you the grain-free disclaimer, let’s talk about dairy-free and no refined sugar baking. Once again not having dairy or refined sugar in your baking recipe will change the texture and flavor. I promise friends, although it’s different, it’s a tasty different.

I substituted coconut oil for butter and honey and pure maple syrup for sugar. My Paleo chocolate fudge cupcakes are super moist and super rich. Packed full of the chocolate fudge flavor you crave.

Chocolate Fudge Frosting

Now let’s talk about the fudge frosting. Honestly, this was the hardest part of the recipe for me. A frosting made with no butter and no sugar was hard for me to imagine. Most Paleo recipes call for coconut cream or palm shortening, which I did not have.

One recipe that I found used avocados. Yes, you heard me right, avocados! I always have avocados in my kitchen, so I thought I would give it a try.

I adapted the recipe because our family likes things on the sweeter side. I was so surprised how glorious the fudge frosting turned out! My kids were super skeptical at first, but once they tried it, they said it tasted like real frosting and they could not taste the avocado at all.

Pro Tip: When I pipe frosting onto cupcakes I use a trick where I line a large cup with the piping bag. It makes the process much less messy! My favorite frosting tip is the Wilton 1M. 

So what did my hubby think? He ate one as soon as he walked in the door! Oh, and then he had another one right after dinner. So I would say that my new adventure into grain-free baking was a success.

If you are needing to make a change to the Paleo diet or a grain-free diet for health reasons or just want to try a new type of gluten-free baking, I promise my recipe for Paleo chocolate fudge cupcakes will not disappoint you.

More Cupcake Recipes To Try

Looking for more Paleo recipes? 

Did you make this recipe? Please give it a star rating below!★

4.54 from 13 votes

Paleo Chocolate Fudge Cupcakes {Dairy-Free, Gluten-Free, Grain-Free}

Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes
My easy and super moist Paleo chocolate fudge cupcakes will satisfy your chocolate cake cravings. Made with simple and healthy ingredients. Gluten-free, dairy-free, grain-free and no refined sugar. Yes, even the glorious chocolate fudge frosting!
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Ingredients 

Cupcakes:

  • 1/2 cups almond flour
  • 1 1/2 cup coconut flour
  • 1 teaspoon baking soda
  • 1/4 teaspoon salt, I like Pink Himalayan Salt
  • 1 teaspoon ground cinnamon
  • 1 cup coconut oil, melted
  • 1 cup cocoa powder
  • 1 cup water
  • 1 tablespoon pure vanilla extract
  • 3 eggs
  • 3/4 cup honey
  • 1 cup no sugar added applesauce

Frosting:

  • 1 ripe avocado
  • 3 tablespoons cocoa powder
  • 2 teaspoons pure vanilla extract
  • 4 tablespoons pure maple syrup
  • pinch salt , I like Pink Himalayan Salt

Instructions 

Cupcakes:

  • Pre-heat oven to 350° F.
  • Combine flours, baking soda, salt and cinnamon in a large mixing bowl.
  • In a small pan melt the coconut oil. Add the cocoa powder and water and stir until all the ingredients are combined.
  • Pour the hot oil mixture into the dry mixture and mix together on low speed, either with a stand-up mixer or hand mixer.
  • Add the eggs, applesauce, pure vanilla extract and honey to the batter and mix until fully combined.
  • Add the batter to lined cupcake pans. The batter will be thick and sticky. Fill the cupcake cups all the way to the top. If you are not using baking cups, spray cupcake pans with cooking spray.
  • Bake for 20-25 minutes. Watch the cupcakes, because all ovens are different. Place a toothpick in the center of a cupcake to see if it fully cooked.
  • Cool completely before frosting.
  • Store in an airtight container. (These are even better the second day!) Frost the cupcakes as you eat them. Place remaining frosting in the refrigerator.

Frosting:

  • Add the all of the ingredients into a food processor or blender. Blend until completely smooth.
  • Chill the frosting in the fridge until ready to use.
  • If you are going to pipe the frosting on the cupcakes (like I did) put the frosting in the piping bag and place in the freezer so it can firm up a bit.
  • If you are not piping the frosting, frost the cupcakes as you eat them. Place remaining frosting in the refrigerator.
  • Pro Tip: When I pipe frosting onto cupcakes I use a trick where I line a large cup with the piping bag. It makes the process much less messy! My favorite frosting tip is the Wilton 1M. 
  • Enjoy!

Notes

Pro Tip: When I pipe frosting onto cupcakes I use a trick where I line a large cup with the piping bag. It makes the process much less messy! My favorite frosting tip is the Wilton 1M
Store in an air-tight container. Frost the cupcakes as you eat them. Place remaining frosting in the refrigerator.
Mama says, “Check all of your labels!”
Did you make a recipe? Tag @mamaknowsglutenfree on Instagram, Facebook or @mamaknowsgf on Twitter! I would love to see what you created!

Nutrition

Serving: 1cupcakeCalories: 131kcalCarbohydrates: 20gProtein: 3gFat: 5gSaturated Fat: 2gCholesterol: 20mgSodium: 96mgPotassium: 132mgFiber: 5gSugar: 12gVitamin A: 45IUVitamin C: 1mgCalcium: 19mgIron: 1.1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Course: Dessert
Cuisine: American
Tried this recipe?Mention @mamaknowsglutenfree or tag #mamaknowsglutenfree!


About Audrey Roberts

I'm Audrey Roberts, a busy mama of four and I love sharing the recipes that I make for my family. I make gluten-free family-friendly recipes that are simple and delicious that you can too! I use easy to find ingredients that won't break your budget. You will also find dairy-free options and Paleo recipes. I am also the author of The Everything Gluten-Free & Dairy-Free Cookbook, which is an Amazon Best Selling Cookbook in the US and Internationally. Living gluten-free since 2010. I hope by me sharing my journey it may help you with yours.

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4.54 from 13 votes (3 ratings without comment)
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Jen
May 7, 2025 4:25 pm

Turned out dense and bland. Ate one and threw the rest away, this is going to be a pass for me.

Carolyn
November 4, 2024 12:10 am

Will this recipe still work if the chocolate is left out? I need to make white cupcakes also low in sugar.
Thanks!

Sam - Mama Knows Gluten Free
November 13, 2024 10:01 am
Reply to  Carolyn

Hi Carolyn, we have not tried making this recipe without the cocoa powder, but you would need to replace it with more flour to achieve a cohesive batter!

Deb
May 27, 2023 10:44 am

Went ahead and made these today and they are amazing! Definitely a keeper recipe. My daughter in law is GF and my son is trying to cut out as much sugar as possible from his diet so this recipe covers both!! Thank You SO MUCH for sharing! ❤️

Agatha
April 24, 2020 9:04 am

Thank you for this! Just put them in the oven! Can’t wait to try and for my two year old to dig in! Thanks for sharing!

V.Lev
October 28, 2019 4:12 pm

These chocolate fudge cupcakes taste divine my sister recently went on a paleo diet and has been craving chocolate cupcakes for some time now, I made a batch of these and simply loved them I’m going to make another batch for her I’m sure she’ll love them to! Thank you for sharing.

Audrey
October 29, 2019 11:48 am
Reply to  V.Lev

Thank you so much V for teh awesome 5-star recipe review! I am so happy that your sister enjoyed the Paleo cupcakes. You are so welcome, I love sharing what I make for my family. Thanks again!

Anna
July 14, 2019 11:09 pm

I made these for my daughter’s 1st Birthday party! I wanted a healthier option for her 1st Birthday cupcake smash. They are SO DELICIOUS and her reaction to tasting it was priceless. And I felt good letting her enjoy the treat knowing the ingredients were so much healthier. The avocado frosting was amazing too! We will be making these again!

Audrey
July 15, 2019 7:46 am
Reply to  Anna

Thank you so much Anna for the awesome 5-star recipe review! I am so happy that your daughter enjoyed her birthday cupcake. This really made my day! Wishing her the happiest of 1st birthdays. Thank you again!

Trish
June 10, 2019 2:40 pm

Can you recommend an egg substitute? Your recipe says dairy free but there are eggs. Confused. Thanks

Audrey
June 10, 2019 3:51 pm
Reply to  Trish

Hi Tish! Eggs are not dairy. Dairy is food products produced from milk (butter, cheese, yogurt, etc…) I have baked egg-free using Bob’s Red Mill egg replacer if you need to be egg-free as well. I hope you enjoy the cupcakes!

Laura
January 12, 2019 12:40 pm

Hi Audrey,
Thanks so much for recipe.
I was just wondering if I can freeze the cupcakes ?

Audrey
January 13, 2019 9:08 am
Reply to  Laura

Hi Laura! I have never tried to freeze the cupcakes (they never last that long in my house). If you try freezing them can you please let me know how they turn out? You are so welcome I love sharing what I make for my family!

Shaynee
October 22, 2018 12:53 am

Hello, thank you for this recipe. If I were to half the recipe would I half all ingredients? Thank you

Audrey
October 22, 2018 8:30 am
Reply to  Shaynee

Hi Shaynee! Yes if you were to half the recipe just half all of the ingredients. I hope you enjoy the cupcakes!

kate
August 5, 2018 3:44 pm

Hi Audrey,

These cupcakes are great- I made them a few months ago and decided to try them out again today. Only thing I want to share with you is that the ingredient list calls for vanilla extract for the actual cupcakes, but then the instruction do not state when to add vanilla extract- so I’ve forgotten to add that both times now! I don’t think its a big deal, they were great the first time. But just wanted to let you know. Thanks!

Kate

Audrey
August 5, 2018 9:41 pm
Reply to  kate

Hi Kate! Thank you so much for letting me know about the missing step in the recipe instructions. It’s fixed. I am so happy that you have enjoyed the cupcakes!