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Grain-Free Chocolate Cupcakes

A simple grain-free chocolate cupcakes that are naturally gluten-free, low-carb, low-glycemic and perfect for those on a paleo or SCD diet.

At a time that's full of scary costumes, spooky decorations and sugar-laden treats, I could think of no better way to celebrate than with my own sweet contribution.

Gluten-free baking forever changed for me when I started using coconut flour. This flour brings a light and fluffy texture to baked goods that is unmatched with any other gluten-free flour. Fiber-rich coconut flour is low-carb, low-glycemic and naturally gluten-free, not only making it great for those sensitive to gluten, but also those on a paleo or SCD diet, or those with diabetes.

And what better thing to make than grain-free chocolate cupcakes?

Grain-Free Halloween Chocolate Cupcakes | Gluten-Free

Baking with coconut flour can be tricky, but as long as you have the right proportions, your gluten-free baked goods will surely be fabulous. Just remember, eggs are coconut flour's best friend. As a general rule of thumb, I use two eggs with every 1/4 cup of coconut flour (if I'm only using coconut flour in the recipe). With the combination of cocoa powder in this cupcake recipe, I used an extra egg to compensate for the added dry ingredients.

To put it simply, these grain-free chocolate cupcakes are perfect. Everything that you envision when you think of chocolate cupcakes. A springy cake texture, that's still moist and tender, with a  rich chocolate flavor. All topped with a sweet vegan icing. These babies would be great for any occasion, but the fiery orange icing and deep brown (almost black) color, makes them perfect for our Halloween festivities.

Wishing you all a happy and safe Halloween!

Paleo Halloween Chocolate Cupcakes | Gluten-Free

More Healthy Fall Recipes:

Grain-Free Halloween Chocolate Cupcakes

5 from 1 vote
And what better thing to make than grain-free chocolate cupcakes?
author: Alyssa
yield: 6 Cupcakes
Prep: 10 minutes
Cook: 20 minutes
Total: 30 minutes



  • Preheat the oven to 375 degrees F. Line a muffin tin with 6 paper liners (place the liners on the inside of the muffin tin for more consistent baking).
  • Whisk together dry ingredients in a small bowl.
  • In a separate mixing bowl, beat the eggs, honey and 1 tablespoon coconut oil. Add dry ingredients to wet and mix to combine.
  • Spoon batter into the paper liners, filling each about ? of the way full.
  • Bake in the center of the oven for 18 – 20 minutes, until a cake tester inserted into the center, comes out clean.
  • Cool on a wire rack completely before frosting.
  • For the frosting, combine the sweet potato, maple syrup, tapioca starch, remaining 1 tablespoon coconut oil and turmeric in a food processor, and process until smooth. Cool before transferring to a piping bag.
  • Pipe the frosting on the cupcakes and serve immediately.


adapted from Wholepromise


Calories: 205kcal | Carbohydrates: 30g | Protein: 4g | Fat: 8g | Saturated Fat: 5g | Cholesterol: 81mg | Sodium: 198mg | Potassium: 197mg | Fiber: 3g | Sugar: 19g | Vitamin A: 3195IU | Vitamin C: 0.5mg | Calcium: 37mg | Iron: 1.4mg
cuisine: American
course: Dessert, Snack

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42 comments on “Grain-Free Chocolate Cupcakes”

  1. These look so good. Since they require 3 eggs, would there possibly be a substitute for the eggs? I am vegan. Not sure if flax eggs would work.

    1. I don’t think so, sorry! The eggs + coconut flour are the key to making these work… and getting a nice fluffy texture!

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  18. Hi! I’m thinking of making these into mini cupcakes using a mini muffin pan..thoughts? Also, just wondering how long these will last in the refrigerator afterwards and whether I should just frost when we eat them as opposed to frosting all at once? I like to make sweets once a week for my family to enjoy and I’d love it if these lasted a few days. Thanks!

    1. Hi there! I think they would make wonderful mini cupcakes 🙂 What a great idea! I’d say they probably keep for 4 – 5 days. Hope that’s long enough. Definitely report back 🙂

      1. Hi! They were perfect as mini cupcakes…with enough to spare to make a few reg. sized ones. I added some Enjoy Life chocolate chips and they were amazing. Seriously the best cupcakes I’ve made yet since going Paleo (and it’s been awhile!). The frosting was tasty, I added a sprinkle of coconut palm sugar and it added a little crunch, which I’ll definitely do next time too. Thanks again for the awesome recipe!

  19. Wow! I really messed this recipe up. I of course didn’t read the whole thing before diving in, but they still turned out delicious. So here’s what I did. I accidentally added tapioca flour to the muffins instead of the frosting. I can’t have egg yolk so I used 3 egg whites and 2tablespoons of applesauce instead. I can’t eat sweet potato so I used pumpkin instead, but I thought I didn’t read it was for the frosting and I dumped it in the egg mixture. Once I realized what I’d done, I scooped it out, but a able spoon or so was already mixed in. This added to the fact that I have a 1950s oven that burns everything so I have to cook at 100 degrees less for half the time resulted in super moist yummy cakes. For the frosting I used pumpkin, honey and cinnamon with the tapioca, heated it up. It was more like a sauce, but I added blueberries and poured it over the cakes. It was delicious and definitely satisfied my sweet tooth. Thank you for your recipes. It’s been pinned!

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  21. Have you ever tried making this into a cake?I am guessing that I would have to quadruple the recipe to get enough for 2 8″ or 9″ pans. Also, I don’t have any flaxseed on hand. Is there anything I could use to replace it? I could run to the store, but didn’t really want to if I didn’t have to. 😉 TIA

    1. Hi Jennifer! I have yet to try this recipe as cakes, but I think you’re right in assuming that you will have to probably quadruple the recipe to get 2 round cakes. As far as swapping out the flaxseed, I think you could try and nut or seed meal (chia would be the most similar) with similar results. Let me know how it works out for you! This would make a great birthday cake 🙂

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  23. Avatar photo
    Beth @ Tasty Yummies

    Oh my goodness, I love absolutely everything about this recipe. These look soo yummy! That frosting is sooo darn clever, I cannot even stand it!

  24. Avatar photo
    Heather's Creative Concoctions

    These look soo good and I love how you used sweet potato. I will try these if Sandy doesn’t take my power!

    1. Hope you’re staying safe Heather! Let me know if you try the cupcakes – would love to hear how they work for you.

  25. These look amazing. Turmeric is such a great natural food coloring (and cancer fighter). My mom uses it all the time in Indian cooking. I just found your blog, and I love it. I am not gluten free, but I am vegetarian, and I think cooking with any dietary restriction is always an interesting challenge.

    1. Hi Asilia – I LOVED using the turmeric in the frosting – it gives the cupcakes that pop of color that I was looking for. Even though you’re not gluten-free, I do have lots of vegan and vegetarian options on my site.

      Here’s a link to check out: https://www.simplyquinoa.com/category/vegetarian-vegan/

    2. I’m just curious what did you use for the frosting since the recipe does not include it except I assume the turmeric?

  26. I haven’t baked with Quinoa before so will give these a go if I can find the flour here in the UK. They look great for Halloween and really moist!

    1. Hi Maria – these cupcakes actually don’t contain quinoa. It’s the coconut flour that makes these babies so fabulous.

      I do have an ebook coming out in the next few weeks that’s all about baking with quinoa. It has 25 recipes, most of which are not on the site and gives tips for making healthy baked goods using quinoa. I’m offering my email or RSS subscribers 20% off, so I encourage you to sign up and you’ll be getting a coupon in the your email.

      Here’s a post that has more information about the book: https://www.simplyquinoa.com/cookbooks/