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!

5.0 from 1 reviews
Chocolate Beet Cupcakes
Yields 12-14 cupcakes
Cuisine: Baking
  • 3 medium beets, peeled and diced
  • 2 cups all-purpose gluten-free flour
  • 1 teaspoon xanthan gum (optional)
  • ¼ teaspoon ground cinnamon
  • 2 teaspoons baking soda
  • ½ teaspoon salt
  • 1¼ cups sugar
  • ½ cup Dutch cocoa powder
  • 2 large eggs, beaten
  • 1 teaspoon vanilla extract
  • 2 tablespoons unsweetened applesauce
  • ½ 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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  1. Elisha says

    I made this in March 2013 with great success but left out the xantham gum because I didn’t have any. Recently my doc advised me to lay off chocolate (and other yummy foods) because of GERD. So I made them again today with xantham gum, 1 can of whole beets instead of 3 fresh, and carob powder instead of cocoa powder. They taste okay, but not as good as last year when I used fresh beets and cocoa powder. They have sort of a fake tangy chocolate taste. Not too bad but not the chocolate flavor I’m craving. Definitely best with the cocoa powder! The canned beets worked out very well and was such a big time saver for this busy mom!

  2. Elizabeth says

    Simply Amazing! I made a batch of these the other day using half wheat/half white flour since I didn’t have any gluten free, and they still came out delicious (BTW – I added only about 1/8 cup of water) They are moist, chocolatey and don’t even need anything on top. My son is happy because he gets a chocolate treat, and I feel good because its a healthier alternative AND he’s getting a little extra dose of vegetables! These also came out really well in the mini-muffin pan. Thanks for another great recipe

  3. says

    hello keeley.
    can the eggs be substituted by anything else?
    my daughter is anaphylactic to eggs & nuts amongs any seeds including flax.

    your help is greatly appreciated.

    ps.. we just made your choc. gluten free choc. cake recipe as cup cakes and are hoping they turn out okay.
    desperately need a cup cake recipe as her birthday is right around the corner and she hasnt had cake for her first 2 birthdays :(

    thank you ,

    • Daiane says

      You can use egg replacer (1 tsp + 11/2 tbsp water) or increase the amount of apple sauce, or instead of water use some kind of milk + 1/4 tsp of apple cider vinegar, increase the volume and forget the eggs.

  4. jodie says

    Sounds delicious! I know the point is for them to be gluten free, but for those of us that aren’t GF, will conventional flour work?Thanks!

  5. Elisha says

    I made these last night and the kids love them! And what I like is that they’re not too sweet and they taste a little like dark chocolate….yum!! But it takes a lot of time peeling, dicing and boiling the beets. Do you think you can use canned beets to save time? I know some of the nutrition would probably be lost.

    • says

      Hi Elisha, So glad they enjoyed them! You certainly can try using canned beets just make sure they’re not too wet. Let us know how they turn out next time if you go that route. Thanks for taking he time to comment!!

  6. Michelle says

    I’m new to vegan baking. Would you suggest egg replacer powder or flaxseed and water as a substitute for the eggs ?
    I would LOVE to make these for my family.

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