Chocolate Beet Cupcakes

Need a delicious treat that is gluten- and dairy-free? These chocolate beet cupcakes are moist, full of vitamins, and 100% kid-approved.

Gluten Free Chocolate Beet Cupcakes -

When birthdays happen at school, my daughter needs a treat to take to school that’s safe for her allergies. I’ve become a master at stocking my freezer with goodies that I can have available for an immediate need.

Cupcakes are the perfect vessel to sneak in some vegetables, because many of them add tons of moisture. This delicious cupcake idea came from my local farmers co-op!

Beets are not only considered to be “heart healthy,” but they are also a great source of fiber, vitamin C, and potassium. My daughter particularly loved helping me bake these cupcakes, seeing the beet’s bright color and how they naturally changed the water pigment when boiled. I love finding opportunities to educate her about fresh foods!

Bake and freeze these chocolate beet cupcakes for future treats, enjoy them right now for dessert, or packed as a special surprise for lunch. They’re gluten-, nut-, and dairy-free. Enjoy!

Chocolate Beet Cupcakes

Yields 12-14 cupcakes

  • Author: MOMables
  • Cuisine: Baking


  • 3 medium beets, peeled and diced
  • 2 cups all-purpose gluten-free flour
  • 1 teaspoon xanthan gum (optional)
  • 1/4 teaspoon ground cinnamon
  • 2 teaspoons baking soda
  • 1/2 teaspoon salt
  • 1 1/4 cups sugar
  • 1/2 cup Dutch cocoa powder
  • 2 large eggs, beaten
  • 1 teaspoon vanilla extract
  • 2 tablespoons unsweetened applesauce
  • 1/2 cup warm water


  1. On your stovetop, place the beets into a pot, and cover them with water. Bring the water to a boil, then let them simmer until softened. This will take about 25 to 30 minutes.
  2. Drain the pot, and puree the beets in your food processor or blender until they’re smooth.
  3. Preheat the oven to 350F. Coat muffin tins with cooking spray and set aside.
  4. In a large mixing bowl, blend together the flour, xanthan gum (if using), cinnamon, baking soda, salt, sugar, and cocoa powder.
  5. Add the eggs, vanilla, applesauce, and pureed beets. Mix well.
  6. Slowly add the water, and mix until well combined.
  7. Fill the muffin tin cavities three-quarter full, and bake for 25 to 28 minutes.
  8. Remove from the oven, let them cool for 3 to 4 minutes in the tin, then transfer them onto a cooling rack.
  9. Once they’re cooled, you can freeze them or enjoy immediately!
  10. Feel free to add icing, a glaze, or simply powdered sugar to the tops, if you desire.


If you’ve made successful substitutions to the recipe, feel free to share them below. We test our recipes more than a few times, and what we post on the site are tried-and-true versions.


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About Keeley McGuire

Keeley is our resident allergy friendly contributor. She is a full-time working mom to one little girl who loves her homemade lunches. In her personal blog, KeeleyMcGuireBlog, she shares her gluten free and peanut free recipes, her love for her crockpot, and the occasional craft.