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    Home » Cakes and Cupcakes

    Gluten Free Chocolate Cupcakes

    Published: Jun 23, 2016 Updated: Aug 2, 2022 by Alison Andrews This post may contain affiliate links

    Jump to Recipe
    Gluten Free Chocolate Cupcakes

    Perfectly moist gluten free chocolate cupcakes with a rich chocolate buttercream frosting. So good you’ll never know they’re gluten-free and vegan!

    Gluten-free chocolate cupcakes on a wire cooling rack.

    You know, when I finally cracked the code to gluten-free baking and managed a spectacular gluten free chocolate cake, I was so darn happy about it.

    I mean no one wants to eat a cake that tastes like it’s not quite as good as the original. You want it to just taste like delicious cake.

    Same thing for vegan cake of course, you just want it to taste like cake. Not vegan cake.

    Well, these gluten free chocolate cupcakes are naturally also vegan – I say naturally because, have you seen the name of this blog? But really if you feed them to your non-vegan gluten-eating friends they will have no idea.

    These are just fabulously delicious cupcakes. No one would be the wiser unless you told them. No one will know they’re gluten free. Or vegan for that matter. They’re just like the best cupcakes you’ve ever had. That’s all.

    The texture of these cupcakes, oh my, the texture. So perfectly moist and delicious. And so rich and chocolatey.

    And really they’re a cinch to make too.

    I have a mother and sister who are gluten-free so if they’re coming over for any sort of special occasion, these cupcakes, or the gluten free chocolate cake recipe that they’re based on, are making an appearance!

    Gluten-free chocolate cupcakes topped with chocolate frosting and sprinkles on a wire cooling rack.

    How To Make Gluten Free Chocolate Cupcakes

    You will find full instructions and measurements in the recipe card at the bottom of the post. This is a summary of the process to go along with the process photos.

    • Sift gluten free all purpose flour and cocoa powder into a mixing bowl.
    • Add light brown sugar, baking soda and salt and mix together.
    • Prepare your flax egg by mixing 1 Tbsp ground flaxseeds with 3 Tbsp hot water and allowing to sit for a minute.
    • Add the flax egg, soy milk, vanilla extract, oil, applesauce and vinegar and mix into a batter.
    • Use a hand whisk to get rid of any large lumps (very small ones are fine).
    • Divide the batter evenly between 12 cupcake liners.
    • Place into the oven to bake for 22-25 minutes or until a toothpick inserted into the center of a cupcake comes out clean.
    Step by step process photos of making gluten-free chocolate cupcakes

    Baker’s Tips

    Check the expiry date. Always check the expiry date on your gluten-free all purpose flour mix! Gluten-free flours tend to have a shorter shelf life than regular gluten flours, and on one particular occasion, I didn’t check the expiry date on mine and made my mother a gluten-free birthday cake.

    I then proceeded to question ALL my baking skills when I tasted it! Only to find out that my flour had expired (at least it made me feel good again about my baking skills).

    So check the dates on your flour, especially if you don’t bake super often, it’s likely you need to get a fresh supply.

    Use a gluten free all purpose flour blend. It has to be a blend that is designed to replace regular all purpose flour in baking.

    Chocolate cupcakes topped with chocolate frosting and sprinkles on a wire cooling rack.

    Storing and Freezing

    Keep your cupcakes stored in an airtight container at room temperature for 2-3 days. You can also store them in the fridge in an airtight container for up to 5 days.

    They are also freezer friendly for up to 3 months if you’d like to freeze them. They can be frozen either frosted or unfrosted.

    Chocolate cupcakes on a wire cooling rack.

    More Gluten Free Baking Recipes

    1. Vegan Gluten Free Carrot Cake
    2. Gluten Free Carrot Cake Cupcakes
    3. Vegan Gluten Free Chocolate Cake
    4. Vegan Gluten Free Chocolate Chip Cookies
    5. Vegan Gluten Free Brownies
    6. Vegan Gluten Free Vanilla Cupcakes
    Chocolate cupcake cut in half to show the center.

    Did you make this recipe? Be sure to leave a comment and rating below!

    Frosted gluten free chocolate cupcakes on a wire rack.

    Gluten Free Chocolate Cupcakes

    Perfectly moist gluten free chocolate cupcakes with a rich chocolate buttercream frosting. So good you'll never know they're gluten free and vegan!
    4.74 from 26 votes
    Print Pin Rate
    Course: Cupcakes, Dessert
    Cuisine: American
    Diet: Vegan
    Prep Time: 20 minutes minutes
    Cook Time: 25 minutes minutes
    Total Time: 45 minutes minutes
    Servings: 12
    Calories: 393kcal
    Author: Alison Andrews

    Ingredients

    For the cupcakes:

    • 1 ½ cups Gluten Free All Purpose Flour (204g)
    • ½ cup Cocoa Powder (42g) Unsweetened
    • 1 cup Light Brown Sugar (200g)
    • 1 ¼ teaspoons Baking Soda
    • ½ teaspoon Salt
    • 1 Flax Egg 1 Tbsp Ground Flaxseed Meal + 3 Tbsp Hot Water
    • 1 cup Soy Milk (240ml) or other non-dairy milk
    • 2 teaspoons Vanilla Extract
    • ½ cup Canola Oil (120ml) or Vegetable Oil
    • 2 Tablespoons Applesauce
    • 1 Tablespoon Distilled White Vinegar or Apple Cider Vinegar

    For the Frosting:

    • ⅓ cup Vegan Butter (75g)
    • 3 cups Powdered Sugar (360g)
    • ½ cup Cocoa Powder (42g) Unsweetened
    • 2 teaspoons Vanilla Extract
    • 4 ½ Tablespoons Soy Milk or other non-dairy milk
    Prevent your screen from going dark

    Instructions

    • Preheat the oven to 350°F (180°C). Line a cupcake tray with cupcake liners.
    • Sift the flour and cocoa powder into a mixing bowl and add the brown sugar, baking soda and salt. Mix together.
    • Prepare your flax egg by mixing 1 Tbsp ground flaxseeds with 3 Tbsp hot water and allowing to sit for a minute.
    • Add the flax egg, soy milk, vanilla extract, oil, applesauce and vinegar and mix into a batter.
    • Use a hand whisk to get rid of any large lumps (very small ones are fine).
    • Divide the batter evenly between the 12 cupcake liners.
    • Place into the oven to bake for 22-25 minutes or until a toothpick inserted into the center of a cupcake comes out clean.
    • While the cupcakes are baking, prepare your frosting by adding the vegan butter, powdered sugar, cocoa powder, vanilla and 3 tablespoons of soy milk to the bowl of your stand mixer and starting on low speed gradually increase speed until it's thick and creamy. If it's too thick, add in the remaining soy milk only as much as needed to get the right consistency.
    • As soon as your cupcakes are cooked, move them to a cooling rack to cool completely before frosting.

    Notes

    1. Gluten free all purpose flour. I used Bob’s Red Mill All Purpose Baking Flour but I have tested this recipe with other gluten-free all purpose blends and they have all been perfect. Some blends have had xantham gum in them and some have not, and I have not found a difference in the outcome. As long as it is an all purpose baking blend, it should work well for this recipe.
    2. Storing: Keep your cupcakes stored in an airtight container at room temperature for 2-3 days. You can also store them in the fridge in an airtight container for up to 5 days. 
    3. Freezing: They are also freezer friendly (frosted or unfrosted) for up to 3 months. 

    Nutrition

    Serving: 1Cupcake | Calories: 393kcal | Carbohydrates: 65g | Protein: 4g | Fat: 16g | Saturated Fat: 2g | Polyunsaturated Fat: 4g | Monounsaturated Fat: 8g | Trans Fat: 0.1g | Sodium: 272mg | Potassium: 182mg | Fiber: 5g | Sugar: 49g | Vitamin A: 340IU | Vitamin C: 2mg | Calcium: 73mg | Iron: 2mg
    DID YOU MAKE THIS RECIPE? Rate it & leave your feedback in the comments section below, or tag @lovingitvegan on Instagram and hashtag #lovingitvegan
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    About the Author

    Hi I'm Alison Andrews, I'm the voice and cook behind Loving It Vegan. I love making delicious vegan food and creating vegan versions of all your old favorites, so that you’ll never feel like you’re missing out. Find out more about me here.

    Loving It Vegan is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com. This site may contain some of these links to Amazon.com. If you make a purchase through one of those links, Loving It Vegan will receive a small commission from the purchase at no additional cost to you.

    Reader Interactions

    Comments

    1. Beth says

      January 31, 2019 at 1:05 am

      Getting ready to make the recipe – two questions.
      1) Have you or can you double it? I need more than 12 cupcakes. From the pictures, it also looks like you almost fill the cups near to the top?

      2) Will we really need a full recipe of the icing for only 12 cupcakes or did you have extra?

      Thanks!

      Reply
      • Alison Andrews says

        January 31, 2019 at 10:45 am

        Hi Beth, you should be able to double it without an issue, just be really careful with your calculations and it should be fine. I do fill the liners close to the top, but as you can see they come out with perfect little domes on top. I didn’t have any leftover frosting, I used all of it for these cupcakes, but as you can see it’s piped on fairly generously, I suppose you could use less if you didn’t plan on piping it like this.

        Reply
    2. Vanessa says

      November 08, 2018 at 3:16 pm

      I just followed this recipe to the T and for some reason my sides and bottoms burned! I never burn anything! Maybe it’s the gluten free factor? I took them out at 20 minutes. But when the bottom started burning, the centers weren’t even close to done yet. Any ideas I could try differently? Trying these out for my gluten free friend’s bday. Thanks for any help! Otherwise, the center was delicious ? ?5 stars

      Reply
      • Alison Andrews says

        November 08, 2018 at 4:40 pm

        Hi Vanessa, that’s never happened to me, so my only thought would be that your oven is not calibrated correctly and is burning too hot. If you check with an oven thermometer, it will tell you what your oven really is when you think it’s 350F, then you can adjust accordingly. It’s definitely nothing to do with it being gluten-free, they should not burn at all.

        Reply
        • Vanessa says

          November 08, 2018 at 5:14 pm

          I totally goofed up. I did not mix properly. I fixed my mistake & these are so delicious. ?
          Thank you for the recipe!!! ???5 stars

          Reply
          • Alison Andrews says

            November 09, 2018 at 11:33 am

            So glad to hear! Thanks for the update! 🙂

    3. Paige says

      November 01, 2018 at 11:53 pm

      Do you have to use vinegar?

      Reply
      • Alison Andrews says

        November 03, 2018 at 9:47 am

        It reacts with baking soda so it is a crucial ingredient in this recipe. You could try something like lemon juice instead.

        Reply
    4. Lauren says

      June 07, 2018 at 9:10 pm

      Does the gluten free flour have to contain xanthum gum? Gluten free baking is new to me and I noticed some brands contain it and others do not. Do you personally use xanthum gum in this recipe? Thank you!

      Reply
      • Alison Andrews says

        June 08, 2018 at 7:28 am

        Hi Lauren, when I made this recipe I used Bob’s Red Mill All Purpose Baking Flour, and that particular blend does not contain xantham gum. However, in the interim I have made this recipe with other gluten-free all purpose blends that do contain it. I haven’t noticed any difference in the final result. So as long as it’s an all purpose blend especially for baking, it should be fine whether or not it has xantham gum. All the best!

        Reply
    5. Cindy says

      June 04, 2018 at 6:44 pm

      I’ve made these with a regular chicken egg and they were fabulous!! They rose great, were moist and couldn’t be identified as gluten free! We have many g.f family members and one dairy free. They were a huge hit!!! Thanks for the recipe. I’m sharing the heck out of it!!

      Reply
      • Alison Andrews says

        June 05, 2018 at 7:03 am

        Great to hear it worked out so well Cindy! Thanks so much for posting. 🙂

        Reply
    6. celine says

      May 29, 2018 at 4:09 pm

      Hi Alison, could you use an egg replacer instead of a flax egg? Thanks!

      Reply
      • Alison Andrews says

        May 29, 2018 at 4:46 pm

        Hi Celine, I have only ever tested it with a flax egg, but in theory that should be fine.

        Reply
        • Stephanie says

          October 03, 2019 at 12:10 pm

          I replaced the flax with 3 TBSP of apple sauce. They came out wonderful!

          Reply
          • Alison Andrews says

            October 03, 2019 at 1:30 pm

            Awesome! Thanks for sharing! 🙂

    7. bala says

      May 24, 2018 at 3:13 pm

      hi , can i substitute 1 flax egg to 1 organic egg ? TIA

      Reply
      • Alison Andrews says

        May 24, 2018 at 3:29 pm

        Please see the comment reply above.

        Reply
    8. Amy says

      May 19, 2018 at 3:22 pm

      Hi, thanks for sharing your recipe is sounds like an awesome one to try. I’d like to make it soon though I don’t have a flax egg (not sure what it is) and only regular milk. Can you use an egg and reg. milk as substitutes?

      Reply
      • Alison Andrews says

        May 19, 2018 at 3:49 pm

        Hi Amy, it has never been tested with a regular egg as it was designed as a vegan recipe, the flax egg is linked in the ingredients list to a page with a video which shows you what it is and how to make it, and it’s also described in the recipe instructions. Any milk would be fine, and if you want to try it with a regular egg of course go ahead, but it has not been tested that way. All the best!

        Reply
    9. Vicki says

      May 17, 2018 at 9:51 pm

      My cupcakes were very dense. Should I have mixed them like a muffin mix, that is hardly any whisking? I used a stand mixer as if it was a sponge cake, was this too much do you think? Should I have barely mixed in the wet to the dry? Thanks.

      Reply
      • Alison Andrews says

        May 18, 2018 at 7:49 am

        Hi Vicki, I definitely wouldn’t use a stand mixer to mix the cake batter, you are right, it should just be a quick whisk with a hand whisk until big lumps are gone (tiny lumps are okay). I think this would likely have caused the density, especially if everything else went as planned (flour measures were definitely correct etc). Hope they’re still tasty?

        Reply
    10. Contessa says

      April 15, 2018 at 10:52 am

      Great recipe. So easy. Love this one and your gf vanilla cupcakes too Thankyou. Have shared your recipes and links on my Facebook gluten free and dairy free cooking page. I usedd sunflower oil stead of olive oil ( for a more neutral taste) and baking powder instead of baking soda, different quantity.5 stars

      Reply
      • Alison Andrews says

        April 15, 2018 at 4:35 pm

        Oh great! Thanks so much! And thanks for posting! 🙂

        Reply
    11. Cathie says

      April 09, 2018 at 8:24 am

      Loved them, thank you! It’s so nice for my allergy toddler and I to enjoy a treat every now and then!
      Do they store well in the fridge or freezer? Thanks ?5 stars

      Reply
      • Alison Andrews says

        April 09, 2018 at 10:56 am

        So glad you loved them! 🙂 Thanks for sharing! You can keep them covered in the fridge for up to a week and they will stay good. If you want to freeze them you can do so by individually wrapping them and storing in a sturdy container. They can be frozen for up to 3 months.

        Reply
    12. Tré says

      March 23, 2018 at 5:50 pm

      Can I use coconut sugar instead of brown sugar?

      Reply
      • Alison Andrews says

        March 23, 2018 at 5:59 pm

        Coconut sugar is also granulated so that should be fine as a switch.

        Reply
    13. Nena says

      January 04, 2018 at 12:59 am

      I love this recipe. I make these for every special occasion. I make my own gluten free flour blend but I find that my cupcakes tend to be more like brownies. Heavy and dense but still good. I am curious, what gluten free flour blend do you use or recommend? Do you blend your own? Please let me know. I am using rice flours and tapioca.5 stars

      Reply
      • Alison Andrews says

        January 04, 2018 at 6:42 am

        Hi Nena, I have been a fan of Bob’s Red Mill brand of flours, they have the all purpose gluten-free flour blend which is what I used for these cupcakes. I believe their 1-1 gluten-free flour blend is also very good! 🙂 So glad you like this recipe – thanks for posting! 🙂

        Reply
    14. Mary says

      October 19, 2017 at 3:35 am

      Made these today… delicious! Truly the best vegan, gluten free, chocolate cupcake I’ve ever eaten. Will be making them again for my granddaughter’s birthday party. Thank you for sharing your great recipes.

      Reply
      • Alison Andrews says

        October 19, 2017 at 6:29 am

        That is so fantastic Mary – so glad to hear! 🙂

        Reply
    15. Nicole Elliott says

      October 14, 2017 at 10:37 pm

      WOWZERS!!!!! I’ve been vegan for almost two years, but just ventured into gluten-free. This recipe is fantastic! I’m an avid baker and appreciate a fool-proof recipe. To be honest, I’m not the biggest sweet eater, and found them to be a bit too rich for my taste (my husband and daughter thought they were perfect!) Do you happen to have a white/yellow cake recipe that is similar? Thank you so much for a great cake!4 stars

      Reply
      • Alison Andrews says

        October 15, 2017 at 9:19 am

        Awesome Nicole! Glad it was a hit! I have some gluten-free vanilla cupcakes! So check those out. And of course I’ll be adding more gluten free cake recipes soon! 🙂

        Reply
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