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Healthy Chocolate Muffins (Vegan & Dairy-Free)

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These chocolate muffins are sneaky-healthy. The secret ingredient? Beets! These nutrient-packed root vegetables not only contribute to the incredible texture of these muffins, but it also infuses them with a subtle natural sweetness.

Healthy chocolate muffins with beets

Pureed beets bring a surprising (and very luscious) texture to the mix in these healthy chocolate muffins. Don’t knock it till you try it! I find the balance of rich chocolate and earthy sweetness to be absolutely perfect.

Beets not only add a beautiful and vibrant color to this snack, but they also significantly elevate the nutrition. I’m all about baked goods that are sneaky-healthy.

It’s hard to believe these muffins fall into the category of a healthier baked goods. They’re the perfect midnight snack or quick breakfast on the go.

Looking for more yummy breakfast ideas? Try these pumpkin pancakes, these vegan sweet potato muffins or one of these green smoothies.

Recipe highlights

  • These chocolate muffins are kid-friendly and perfect for an on-the-go breakfast. They have a sneaky healthy ingredient you won’t even notice.
  • Made with flax eggs and oat milk, these muffins are naturally free of dairy and animal products.
  • These muffins are versatile. You can mix up the flavor with chopped nuts or even a Tbsp. of espresso powder for a breakfasty snack.
  • You can freeze these muffins for up to a month. Is there anything better than pulling a midnight snack out of the freezer and having a fresh muffin at any time of the day (or night)?
Healthy chocolate muffins

Ingredients Needed

  • Ground Flax Seed: Flax seeds are the ultimate vegan-friendly egg substitute. They form a gel consistency when mixed with water which helps aid in the structure of this baked good. They’re also very good for you and rich in fatty acids and fiber. More nutrition, please!
  • Water: You’ll need to combine the flax with water to activate the “vegan egg”. These magic flax eggs help the muffins maintain their moisture and texture with no need for animal products.
  • Cooked Beets – Pureed: The sneaky-healthy start of the show in this baked good. These healthy chocolate muffins have pureed beets mixed in to infuse them with natural sweetness. And, how beautiful is that stunning red chocolate? I also love the way these muffins stay incredibly moist with the addition of this veggie.
  • Flour: This is the base of the muffin recipe and provides all the needed structure.
  • Unsweetened Cocoa Powder: I use cocoa powder in so many of my recipes and love the decadent flavor it imparts. Unsweetened powder helps maintain control of the level of sweetness in this recipe.
  • Baking Powder: This is where all that fluffiness and lightness comes from. Baking powder ensures the muffins rise and creates a lovely airy texture.
  • Salt: A small amount goes a long way. Salt helps balance out the sweetness of these muffins while also enhancing the flavor.
  • Packed Light Brown Sugar: Light brown sugar (or substitute coconut sugar if you wish) adds that warm and sweet undertone to these healthy chocolate muffins.
  • Neutral Oil: Oil is needed for moisture and richness. It helps to ensure the muffins are tender and moist. A neutral oil will not impact the flavor – reach for canola, vegetable or avocado oil.
  • Oat Milk: Using oat milk makes these healthy chocolate muffins dairy free. It provides a creamy texture that complements the flavor of these muffins. You can also use soy milk instead.
  • Chocolate Chunks/Chips: Vegan chocolate chunks or chips gives you “bursts” of chocolate goodness throughout each muffin. Choose a high quality option that is vegan and dairy-free. I love the way dark chocolate works in this recipe.

How to make these chocolate muffins

Preheat oven to 350°F. Grease or add paper liners to muffin pan.

In a small bowl, whisk together the ground flax seed along with the water. Stir and set aside for 5 minutes to form.

Use a food processor to puree your cooked beets until smooth.

Combine the flour, cocoa powder, baking powder and salt in a medium bowl, stirring well.

In a separate bowl, combine the beet puree, brown sugar, oil, oat milk and flax egg. Stir until smooth.

Add the dry ingredients until just combined, then, fold in the chocolate chunks.

Divide the batter between all the muffin cups, leaving 1/2 inch of space at the top. Bake for 25 minutes until a skewer comes out with just a few crumbs.

Allow to cool for at least 15 minutes in the pan before serving.

Healthy chocolate muffins

Recipe tips and FAQs

  • For a fruiter flavor, add one ripe banana sliced into the top of each muffin. The flavor complements the cocoa.
  • For extra crunch, try adding 1/2 cup of chopped nuts (such as walnuts or almonds). The nutty crunch allows for a nice contrast to the muffins.
  • If you love the flavor of coffee, you can also add 1 Tbsp. of espresso to the batter. This makes for a very unique “breakfasty muffins”.

How do I store these muffins?

These homemade chocolate muffins can be stored in an air-tight container in the fridge for up to 3 days. However, they taste the best same day. You can also store them in a sealed freezer bag for 1 month.

How do I cook the beets for these muffins?

Boiling or steaming the beets for this recipe works best as a cooking method. This helps to ensure they are soft and moist before pureeing.

I hope you enjoy this recipe for healthy chocolate muffins. They’re sure to satisfy your sweet tooth, whether it be in the morning or at midnight. You can also make a double batch and store these in the freezer for later snacking. They are better than any store bought muffins you can buy.

Craving more healthy recipes?

Healthy Chocolate Muffins (Vegan & Dairy-Free)

Healthy chocolate muffins
These healthy chocolate muffins use a unique ingredient for a moist and decadent treat.
Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes
Serving Size 12 muffins


  • 2 Tbsp. ground flax seed
  • ¼ cup water
  • 1 cup cooked beets pureed
  • 2 cups all purpose flour
  • ½ cup unsweetened cocoa powder
  • 1 Tbsp. baking powder
  • ½ tsp salt
  • ¾ cup packed light brown sugar
  • ¼ cup neutral oil
  • 1 cup oat milk or soy milk
  • ¾ cup chocolate chunks/chips vegan


  • Preheat oven to 350°F. Grease or add paper liners to muffin pan.
  • In a small bowl, combine the ground flax with the water. Stir and set aside for 5 minutes. This will create the "flax egg". It will become a gel consistency.
  • Use a blender, food processor, or an immersion blender to puree cooked beets until smooth.
  • In a medium bowl combine the flour, cocoa powder, baking powder, and salt, stirring to evenly.
  • In a large bowl combine the beet puree, brown sugar, oil, oat milk, and flax egg. Whisk until smooth.
  • Stir in the dry ingredients until just combined. Then, fold in your chocolate chips.
  • Divide batter between the muffin cups, filling to nearly the top. Leave about ½” of space.
  • Bake for 23-27 minutes until a skewer inserted comes out with just a few crumbs (but not wet).
  • Allow to cool for at least 15 minutes in the pan before serving. These are best the same day or can be frozen for up to 1 month. Bring to room temperature before serving.

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    1. Sharon – Measured as cooked and pureed! I will add this to the recipe, thank you. 🙂

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