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chocolate quinoa cupcakes with peanut butter glaze
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5 from 5 votes

Quinoa Chocolate Cupcakes with Peanut Butter Glaze

These QUINOA CHOCOLATE CUPCAKES WITH PEANUT BUTTER GLAZE are perfect for when you're craving a cupcake but you also want to eat healthily. They bake up soft and tender and are topped with a delicious peanut butter glaze. They also happen to be gluten-free, dairy-free, and good for you!
Prep Time20 mins
Cook Time20 mins
cool time30 mins
Total Time1 hr 10 mins
Course: Dessert
Keyword: Cupcakes, Quinoa
Servings: 12
Calories: 255kcal
Author: Crystal Yentzen


For the Chocolate Quinoa Cupcakes

  • 1/2 cup dark chocolate chips* around 3 oz
  • 1/4 cup coconut oil, refined
  • 1 cup quinoa flour*
  • 3/4 cup granulated sugar of choice* see notes
  • 1/3 cup cocoa powder, sifted if lumpy
  • 3 tablespoons tapioca flour*
  • 1 and 1/2 teaspoons baking powder
  • 1/2 teaspoon baking soda
  • 1/2 teaspoon salt
  • 3/4 cup almond milk or milk of choice
  • 2 large eggs

For the Peanut Butter Glaze

  • 1/4 cup coconut oil, refined
  • 1/2 cup peanut butter*
  • 1/4 cup confectioners' sugar* or powdered erythritol for sugar free
  • 1/2 teaspoon vanilla extract


For the Cupcakes

  • Preheat the oven to 350°F (177°C). Line a 12-cup muffin pan with cupcake liners and spray lightly with non-stick spray.
  • Place the chocolate chips and coconut oil in a microwave-safe bowl. Microwave on high for 20 seconds. Remove from the microwave and whisk together until thoroughly combined. Continue microwaving for 20-second intervals until the mixture is smooth. Set aside. Or, if you prefer not to use the microwave, you can fill a saucepan with 1-2 inches of water. Place on the stovetop and bring to a boil. Place a slightly smaller, heat-safe bowl on top of the saucepan. Place the chocolate chips and coconut oil in the smaller bowl and mix frequently until the chocolate is melted and the mixture is smooth.
  • Whisk the quinoa flour, granulated sugar, cocoa powder, tapioca flour, baking powder, baking soda, and salt together in a large bowl until thoroughly combined. Set aside.
  • In a medium-sized bowl, whisk the eggs, almond milk, and vanilla extract together. Slowly whisk in the chocolate/coconut oil mixture.
  • Pour the wet mixture into the dry mixture and stir together until just incorporated.
  • Spoon the batter into the cupcake liners 2/3 of the way full and bake for 18-20 minutes or until a toothpick inserted into the center comes out (mostly) clean. Allow to cool for 10 minutes before transferring them to a wire rack to cool completely.

For the Peanut Butter Glaze

  • Using a stand mixer fitted with a paddle attachment or a hand mixer beat the peanut butter and coconut oil together until thoroughly combined and smooth (about 3-4 minutes). Add the confectioners' sugar and vanilla extract, and beat on low for 30 seconds. Then increase to high for an additional 2 minutes or until smooth and creamy.
  • Transfer the glaze to a bowl and dip the tops of the cupcakes in the peanut butter glaze. The cupcakes can be eaten as is or if you prefer the glaze to set, you can transfer them to the refrigerator for 30 minutes. Allow them to sit at room temperature for a few minutes after removing them from the refrigerator for the best flavor.


  1. Dark Chocolate Chips- To keep these brownies dairy-free, I used Enjoy Life chocolate chips, which are dairy-free. You can certainly use any chocolate chips that you prefer.
  2. Quinoa Flour- Quinoa flour is sold on Amazon, some supermarkets, and health stores. It is also super easy to make at home. Check out my step-by-step instructions.  
  3. Sugar of Choice– You can use regular granulated sugar or granulated erythritol (like I did) for sugar-free. Please note granulated erythritol is about 70 percent as sweet as sugar, so you may want to add a little extra. Coconut sugar is another great option. 
  4.  Tapioca Flour- Tapioca flour keeps the cupcakes light and airy. I use this brand and, it's pretty easy to find. If you can't find it,  you can substitute half the amount of cornstarch. 
  5. Peanut Butter- Be sure to use shelf-stable peanut butter for the glaze such as Jiffy Natural. While I love homemade and all-natural peanut butter for eating at home, they aren't ideal for this peanut butter glaze. The oil tends to separate and can cause the glaze to be a bit runny. 
  6. Confectioners' Sugar- To sweeten the peanut butter glaze, you can use regular confectioners' sugar or you can use a powdered sugar-free option. There are so many on the market now. I would recommend either powdered erythritol, such as Swerve, or a powdered monk fruit sweetener, which is what I used.
  7. Store the cupcakes covered, at room temperature for up to a day, or in the refrigerator for up to five days. 


Calories: 255kcal | Carbohydrates: 18g | Protein: 6g | Fat: 19g | Saturated Fat: 12g | Polyunsaturated Fat: 2g | Monounsaturated Fat: 4g | Trans Fat: 1g | Cholesterol: 31mg | Sodium: 236mg | Potassium: 216mg | Fiber: 2g | Sugar: 6g | Vitamin A: 46IU | Vitamin C: 1mg | Calcium: 79mg | Iron: 1mg