These Beetroot Chocolate Muffins are perfectly sweet, easy to make and full of good-for-you ingredients. Made from pureed beets, Greek yogurt, white whole wheat flour, cocoa powder and naturally sweetened with maple syrup. These nutrient-dense muffins are kid-friendly and are perfect for breakfast, dessert or a snack.

A chocolate beetroot muffin on a cupcake liner with a bite taken out of it.

Vegetable muffin recipes are kinda what put me on the map and is how so many of you have found me and my veggie-loading ways. And, luckily, you love how muffins are a magical (though unexpected) vehicle for getting more veggies in as much as I do!

You all have been loving my beet pancakes and beet brownies for years, so it was time to add a beet muffin recipe to the mix. It took some time to perfect the recipe and balance out the earthy flavor that some may feel iffy about when it comes to beets, but I think I have made another recipe that is sure to become a regular in many of your houses.

These chocolate muffins are super easy to whip up, super tasty, kid-approved and nope, you can’t tasty the earthiness of the blended beets! Naturally sweetened, made with white whole wheat flour, these beetroot muffins also have a boost of protein from Greek yogurt and eggs! They are so chocolaty, delicious, fluffy, and perfectly moist. Making a batch of 12 muffins, this recipe is perfect to make as part of meal prep or for stocking up your freezer. Bonus: they are done, start to finish, in 30 minutes!

Ingredients for beetroot chocolate muffins portioned out in bowls and arranged on a white table.
Ingredients: oil, maple syrup, white whole wheat flour, plain Greek yogurt, cooked beets, eggs, chocolate chips, baking powder, baking soda, cocoa powder, vanilla, and salt.

How to cook beets for these muffins

Cooking your beetroot for this muffin recipe is going to help cut the earthy flavor that many people find off putting about beets. Plus, it will enhance and bring out this beautiful root veggie’s natural sweetness and, thus, adding more sweetness to these muffins.

Time saving hack! Lots of grocery stores have pre-cooked beets in their fridge or freezer section. You can grab some of those to use in this Chocolate Beetroot Muffin recipe to make life and this recipe a little easier.

Can I make these beet muffins without cocoa powder?

You will need to replace the cocoa powder in this recipe with extra flour so that the dry and wet ingredients balance out. If you are hoping to achieve a pink muffin, beets are tricky when baking. They often turn brown in baked goods instead of holding onto their vibrant pink color.

Can these Chocolate Beet Muffins be made vegan?

You can replace the chicken eggs with 2 flax eggs in these beet muffins.

To replace the Greek yogurt, use a dairy-free yogurt like a coconut yogurt or cashew yogurt.

Also, make sure whatever chocolate chips you are using are also dairy-free.

Can I make these beet muffins gluten free?

If you need these beetroot muffins to be gluten free, I suggest using a cup-for-cup gluten free flour blend like Bob’s Red Mill. I have found it to be wildly successful in similar recipes.

Tips and tricks for the best muffins

Let them cool for a bit before enjoying. 

While these Beetroot Chocolate Muffins are so tasty when warm and fresh from the oven, resist the urge to eat these muffins right away. Let them cool for 10-15 minutes.

Why? Because baked goods are still cooking when they are removed from the oven. As they cool, these muffins will firm up and finish setting. Biting into one of these muffins might make you think they are soggy in the middle and need longer to bake, when they actually don’t.

Don’t over mix the batter. 

One of my favorite things about these beet muffins is how fluffy they are. The key to that fluff is to mix the wet and dry ingredients together until JUST combined. Over mixing can lead to dense, flat muffins. Boooooo! No one wants that, so don’t over mix!

Suggested Adaptations

  • Make them gluten free. Use a cup-for-cup gluten free flour mix in place of the flour in this recipe.
  • Need egg-free? Make a flax “egg” by mixing 2 tablespoons of ground flax with 5 tablespoons of water. Set aside for 5 minutes then use in recipe in place of the eggs.
  • Make these beet muffins dairy-free. You can use a dairy-free yogurt like a coconut yogurt or cashew yogurt.

How to store these muffins

These Beetroot Chocolate Muffins can hang out on your counter for a day, but if you plan to enjoy them over several days, pop them in the fridge! Keeping them in an airtight container in your refrigerator will help to keep these moist muffins fresh longer and prevent molding.

Alternatively, you can freeze these muffins in an air-tight, freezer-safe container for up to a month.

More beet-loaded recipes

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Chocolate beetroot muffins on a white table. One is turned on its side and the others are blurred
4.83 from 23 votes

Moist Beetroot Chocolate Muffins

Yield: 12 servings
Prep Time: 10 minutes
Cook Time: 18 minutes
Cuisine: American
Course: Breakfast, Dessert
These Beetroot Chocolate Muffins are perfectly sweet, easy to make and full of good-for-you ingredients. Made from pureed beets, Greek yogurt, white whole wheat flour, cocoa powder and naturally sweetened with maple syrup. These nutrient-dense muffins are kid-friendly and are perfect for breakfast, snack, or as a healthier dessert.


  • 2 large eggs
  • 4 ounces beets, cooked and peeled. About ½ cup pureed
  • ¼ cup avocado oil or melted coconut oil
  • ½ cup maple syrup
  • 2 teaspoons vanilla extract
  • ½ cup plain Greek yogurt
  • cups white whole wheat flour
  • ¼ cup unsweetened cocoa powder
  • ½ teaspoon baking soda
  • 1 teaspoon baking powder
  • ½ teaspoon salt
  • ¼ cup chocolate chips, plus extra for topping


  • Preheat your oven to 375℉ and line a 12-hole muffin tin. Set aside.
    12-hole muffin tin lined with cupcake liners
  • In your blender, combine cooked and peeled beets, eggs, oil, maple syrup, yogurt, and vanilla. Blend until beets are totally pureed. Set aside.
  • In a large bowl, mix together flour, cocoa powder, baking soda, baking powder, and salt until combined.
    Dry ingredients for chocolate beetroot muffins being stirred together in a bowl with a wooden spoon
  • Pour contents of blender into the bowl with dry ingredients. Stir together with a spoon or spatula until just combined, being careful not to over mix. Over mixing can lead to dense muffins, so mixing until just combined is important for achieving fluffy muffins.
    Fold in chocolate chips.
    Blender beetroot mixture being stirred together with dry ingredients for beetroot muffins in a bowl with a wooden spoon.
  • Divide batter evenly between the prepared muffin tin compartments and top with additional chocolate chips, if desired.
  • Bake in preheated oven for 18 minutes or until a toothpick inserted into the middle comes out clean.
    TIP: If you have a kitchen thermometer, bake until your muffins are 200℉ in the center. This will ensure they are cooked through but aren't over baked, which can result in a dry muffin.
    Baked chocolate beetroot muffins in a muffin tin.
  • Let cool 10 minutes before transferring the muffins to a wire cooling rack and/or enjoying. Allow leftovers to cool completely before storing in an air-tight container in your fridge for 4-5 days or in your freezer for up to a month.
Serving: 1muffin, Calories: 166kcal, Carbohydrates: 23g, Protein: 4g, Fat: 7g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 0.003g, Cholesterol: 32mg, Sodium: 203mg, Potassium: 125mg, Fiber: 2g, Sugar: 11g, Vitamin A: 54IU, Vitamin C: 0.5mg, Calcium: 65mg, Iron: 1mg