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    Home » Baking Recipes » Cakes » Gluten-Free Chocolate Quinoa Cupcakes

    Gluten-Free Chocolate Quinoa Cupcakes

    Published: Feb 2, 2024 by Elaine - 19 Comments

    Jump to Recipe Print Recipe

    These Gluten-free Quinoa Chocolate Cupcakes are a delicious twist on a classic chocolate treat. Moist, rich, and completely flourless, these cupcakes boast a luscious dark chocolate flavor and can be prepared without refined sugar. Topped with a heavenly whipped chocolate coconut milk frosting, these cupcakes are perfect for birthdays or any special occasion!

    3 quinoa chocolate quinoa cupcakes in yellow cupcake cases.
    Jump to:
    • ❤️ Why you'll love these quinoa cupcakes
    • 🛒 Ingredients and substitutions
    • 🔪 Instructions
    • How to make whipped chocolate coconut frosting
    • 🔁 Possible Variations
    • 👍🏼 Helpful Tips to make quinoa chocolate cupcakes
    • ❓Reader's Questions
    • Storage and freezing instructions
    • 🗒 More gluten-free cake and cupcake recipes
    • 📖 Recipe

    ❤️ Why you'll love these quinoa cupcakes

    • Dark, Rich Chocolate: Indulge in dark, rich chocolate in every bite.
    • Moist and Tender: These cupcakes promise a moist and tender texture that satisfies your dessert cravings.
    • Plant-Based Milk Option: The recipe accommodates any type of milk, whether plant-based or dairy.
    • Gluten-Free Goodness: Enjoy a gluten-free cupcake without compromising on taste.
    • An alternative to baking a cake. Cupcakes offer individual portions, making them convenient for serving and portion control compared to baking a whole cake. Additionally, cupcakes allow for easy customization and are perfect for special occasions.

    You'll find more popular gluten-free cupcake recipes here, including Carrot Cake Cupcakes, Almond Flour Banana Cupcakes with Cream Cheese Frosting, and Strawberry Shortcake with Vanilla Cupcakes.

    🛒 Ingredients and substitutions

    You'll find a complete list of ingredients with amounts in the recipe card below. But before we get to the full recipe, here are a few notes about some of the key ingredients.

    • cooked quinoa: Quinoa can increase by 3 times when cooked, so you'll need to cook ⅔ cup of dry quinoa with a little less than 1 ⅓ cups of water.
    • milk: You can use any type of milk, plant-based or dairy milk.
    • butter: you can use all butter or a combination of butter and coconut oil
    • sugar: I've tested this recipe several times with both granulated sugar or coconut sugar.
    • cocoa powder: unsweetened, for that rich chocolatey goodness.
    overhead view of 5 quinoa chocolate cupcakes on a plate.

    🔪 Instructions

    Here's an overview of what you'll do to make this recipe perfectly. You'll find complete instructions in the recipe card at the end of this post.

    1. Cook and Cool Quinoa: Start by cooking quinoa and letting it cool while preparing other ingredients.
    2. Prepare Baking Pans: Decide whether you'll make muffins, regular cupcakes, or cakes. Prepare pans accordingly. This recipe will make 18 muffins or 12 regular muffins and 18 mini muffins. Alternatively, it will make two 8-inch round cakes or one 9 x 13-inch cake.
    3. Blend Wet Ingredients: Combine milk, eggs, and vanilla in a blender; add cooled quinoa, melted butter, and coconut oil.
    4. Sift and Mix: Sift sugar, cocoa, baking powder, and baking soda; add blended ingredients to the dry ingredients to create the batter.
    5. Bake and Frost: Fill muffin tins, bake, and frost with delicious whipped chocolate coconut milk frosting.
    wet ingredients in a blender, dry ingredients in a bowl
    1. Combine the wet ingredients in a blender and the dry ingredients in a bowl.
    pouring wet ingredients into dry ingredients in a bowl
    2. Add the wet ingredients to the dry ingredients.
    Combining wet and dry ingredients for chocolate quinoa cupcakes.
    3. Stir until well combined.
    filling mini muffin tins
    4. Fill muffin tins ¾ full and bake.

    How to make whipped chocolate coconut frosting

    1. First, melt the chocolate chips in a glass bowl suspended over simmering water.
    2. Remove the bowl from the heat, then stir in the hardened portion of a can of coconut milk.
    3. Stir until it has melted and is well combined, and then allow it to cool completely before whipping it.
    4. Chill it in the fridge.

    Tip: If you make sure to wait until it is completely chilled and beginning to harden before you whip it, you'll be happy with the results. It holds its shape and makes decorating with a piping bag a breeze. Some brands of coconut milk will become firm faster than others.

    If you find it has hardened too much to whip, let it sit at room temperature for a few minutes until slightly softened.

    adding coconut milk to melted chocolate
    1. Add hardened coconut milk to melted chocolate.
    stirring chocolate coconut milk frosting
    2. Stir until no lumps of coconut milk remain.

    🔁 Possible Variations

    I've made this recipe many times, as cake, as muffins, and as cupcakes and it's always popular. I also like to make these as mini cupcakes for those who want a tiny taste!

    Mini chocolate quinoa cupcakes with chocolate coconut frosting and sprinkles on a white plate.

    👍🏼 Helpful Tips to make quinoa chocolate cupcakes

    • Prepare Ahead: Chill a can of full-fat coconut milk in the refrigerator for 24 hours.
    • Cook and Cool Quinoa: Please note that the recipe requires 2 cups of cooked quinoa, not dry. Cook ⅔ cup of dry quinoa in 1 ⅓ cups of water to yield 2 cups of cooked quinoa. Measure the cooked quinoa before adding it as sometimes it yields a little more than 2 cups.
    • Sugar Choice: Opt for either granulated sugar or coconut sugar based on your preference.
    • Use a Blender: High-speed blenders like Vitamix or Blendtec ensure a smooth batter without quinoa seeds.
    • Expect Flat Cupcakes: These cupcakes might not have a highly rounded dome but can be enhanced with frosting.

    ❓Reader's Questions

    Is quinoa just a trendy food?

    While quinoa gained popularity with the Quinoa 365 cookbook in 2010, it is not merely a trend. An ancient crop grown in the Andes, quinoa offers gluten-free, nutrient-packed goodness, making it a timeless and nutritious choice.

    Storage and freezing instructions

    • To Store: Refrigerate frosted cupcakes in an airtight container.
    • To Freeze: Freeze in an airtight container for up to 3 months, ensuring yourself a chocolate treat whenever cravings strike.

    Serve these flourless chocolate cupcakes and wait for chocolatey smiles all around!

    🗒 More gluten-free cake and cupcake recipes

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      Gluten-Free Spiced Applesauce Cake
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      Gluten-Free Pumpkin Pecan Coffee Cake with Caramel Sauce
    • Flourless Lemon Ricotta Cake with blackberry sauce.
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    See more Cakes →

    When you make these gluten-free quinoa chocolate cupcakes, please leave a comment and a star rating below. Thanks in advance! Subscribe to my newsletter and receive new recipes delivered straight to your inbox once a week.

    This recipe was originally published in 2016. It has been updated with extra information and new photos.

    📖 Recipe

    quinoa chocolate cupcakes in yellow cupcake cases.

    Gluten-free Quinoa Chocolate Cupcakes

    These Chocolate Quinoa Cupcakes are rich, uber-chocolately and gluten-free.
    Print Pin Rate
    Course: Baked Goods, Desserts
    Cuisine: American
    Diet: Gluten Free
    Prep Time: 40 minutes minutes
    Cook Time: 27 minutes minutes
    Total Time: 1 hour hour 7 minutes minutes
    Servings: 18
    Calories: 285kcal
    Author: Elaine
    Prevent your screen from going dark

    Ingredients

    • 2 cups cooked quinoa, see note below
    • ⅓ cup milk, plant-based or dairy milk
    • 4 large eggs
    • 1 teaspoon vanilla extract
    • ½ cup melted butter
    • ¼ cup melted coconut oil
    • 1 ¼ cups sugar granulated sugar or coconut palm sugar
    • 1 cup unsweetened cocoa powder
    • ½ teaspoon baking soda
    • 1 ½ teaspoons baking powder
    • ½ teaspoon sea salt

    Whipped Chocolate Coconut Cream Frosting

    • 1 14 ounce can full-fat coconut milk, refrigerated overnight
    • 2 cups chocolate chips* use Enjoy Life brand for paleo diet

    Instructions

    • Cook ⅔ cup dry quinoa in 1 ⅓ cups of water. ( ⅔ cup of quinoa cooked in 1 ⅓ cups water will yield approximately 2 cups of cooked quinoa.) Spread out on a baking sheet to cool.
    • Heat oven to 350°F. Line 12 to 18 muffin tins with parchment paper liners or 12 muffin tins and 18 mini muffin tins. Alternatively, line two 8″ round pans or one 9 x 13″ pan with parchment paper.
    • Mix the milk, eggs and vanilla in a blender or food processor.
    • Add the cooked and cooled quinoa, butter, and coconut oil to the blender. This is where a high-speed blender like a Vitamix or a Blendtec comes in handy, as it will grind the cooked quinoa, preventing a lumpy texture in the cooked cake.
    • Sift the sugar, cocoa, baking powder, baking soda and sea salt in a large bowl.
    • Add the wet ingredients from the blender to the dry ingredients in the bowl and mix until thoroughly combined. Fill lined muffin tins ¾ full, spreading to the edges.
    • Bake at 350 degrees for 24-27 minutes or until toothpick inserted comes out clean.Remove, let cool in tins for 10 minutes, then transfer to a cooling rack. Remove the parchment paper liners. Let cool before frosting with whipped chocolate coconut cream frosting.

    Whipped Chocolate Coconut Cream Frosting

    • Melt chocolate in a bowl over, not in, simmering water.
    • Remove the can of coconut milk from the refrigerator. Carefully open it and scoop the hardened milk from the can into the chocolate, saving the liquid for another use. Stir until melted and combined. Remove from heat, let cool.
    • When completely cool and just beginning to harden slightly, beat with an electric mixer until light and fluffy.
    • Frost. Makes 18 cupcakes or 12 cupcakes and 12 - 18 mini cupcakes.

    Notes

    • To Store: Refrigerate frosted cupcakes in an airtight container.
    • To Freeze: Freeze in an airtight container for up to 3 months, ensuring yourself a chocolate treat whenever cravings strike.

    Nutrition

    Calories: 285kcal | Carbohydrates: 33g | Protein: 5g | Fat: 17g | Saturated Fat: 12g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 2g | Trans Fat: 1g | Cholesterol: 55mg | Sodium: 182mg | Potassium: 286mg | Fiber: 3g | Sugar: 21g | Vitamin A: 221IU | Vitamin C: 1mg | Calcium: 98mg | Iron: 1mg
    Tried this Recipe? Pin it for Later!Mention @enessman or tag #flavourandsavour!

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    Reader Interactions

    Comments

    1. Stephanie

      January 24, 2024 at 9:58 am

      Hi! I was wondering if I should use dutch processed or natural cocoa powder? thanks so much!

      Reply
      • Elaine

        January 24, 2024 at 11:13 am

        Hi, natural cocoa powder works well in this recipe as it is balanced by the combination of baking soda and baking powder. Thanks for your question!

        Reply
        • Stephanie

          February 09, 2024 at 1:47 pm

          5 stars
          Thanks so much for your reply! I just wanted to let you know that I made them before I heard back from you and used the Dutch Processed... and it worked out fine! 🙂 The recipe is really delish, and I think tastes even better the next day. Thanks again!

        • Elaine

          February 11, 2024 at 11:32 am

          Hi, Thanks so much for letting me know! Happy to hear you liked these, too!

    2. Savannah

      March 04, 2023 at 1:06 pm

      Could I use a flaxseed/chia seed substitute for the eggs?

      Reply
      • Elaine

        March 04, 2023 at 1:22 pm

        Hi Savannah, I haven't tested that myself so I can't guarantee results. This recipe calls for 4 eggs. They're needed to provide the "lift" to help rise the batter, as there is no gluten in the recipe. Flax eggs work in some recipes, but they don't bind or rise during baking as chicken eggs do. If you do try it, please let me know! Thanks for your question.

        Reply
    3. Laura

      May 06, 2022 at 12:40 pm

      5 stars
      Love these! They are moist and chocolately -- you'd never guess they are gluten free

      Reply
      • Elaine

        May 06, 2022 at 1:47 pm

        Thanks! I just made another batch of these and froze half of them. Thanks for taking the time to comment!

        Reply
    4. Penelope

      June 28, 2020 at 12:54 pm

      Can’t wait to try your recipe! Any thoughts on using date sugar?
      Thanks

      Reply
      • Flavour & Savour

        June 28, 2020 at 1:10 pm

        I haven't tried it myself, but date sugar can usually be used as a 1:1 replacement for coconut sugar or granulated sugar. It should work just fine! It will probably give it a rich flavour, too. Let me know if you try it.

        Reply
    5. Laura

      November 19, 2017 at 8:51 am

      5 stars
      Can this be made in cake pans?

      Reply
      • Flavour & Savour

        June 28, 2020 at 1:06 pm

        Yes, it can. It may take a little longer to bake. You'll know it's done when a toothpick inserted in the center comes out clean.

        Reply
    6. Lisa Solonynko

      April 10, 2017 at 7:41 am

      I am so excited to make this. I have a quick question before I get started. Are you using Imperial, Metric or US Standard measurements. Since this is a cupcake recipe, I want to make sure I get the measurements right. Thanks so much, I can't wait to make this for Easter.

      Reply
      • Flavour & Savour

        April 10, 2017 at 10:44 am

        Hi Lisa,
        I use US Standard measurements. Note, however, that the can of coconut milk I used was 14 oz. In Canada, as you know, they are sometimes only marked in millilitres. Many cans of different brands of coconut milk are 400 ml which is not an exact conversion. However, in the frosting recipe, it really won't make any difference.

        Reply
    7. Laura

      March 13, 2016 at 12:31 pm

      5 stars
      Uber-chocolatey is right! These are delicious.

      Reply
      • Flavour & Savour

        March 13, 2016 at 12:36 pm

        Thanks Laura! Can we ever have too much chocolate?

        Reply
        • Laura

          March 14, 2016 at 12:23 pm

          5 stars
          Never!

    8. Bethany @ athletic avocado

      March 03, 2016 at 5:08 pm

      Adding quiona in place of flavor is GENIUS! Not only does it up the nutritional value, but Im sure it lends the perfect texture to these cupcakes!

      Reply
      • Flavour & Savour

        March 04, 2016 at 7:35 am

        Thanks Bethany, I was concerned that there would be little quinoa lumps in it, but no--the blender took care of that! Thanks for your comment.

        Reply
    5 from 5 votes

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