Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (2024)

These secretly healthy carrot cake cupcakes are moist, fluffy, and topped with thick vegan cream cheese frosting!

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (1)

The best healthy carrot cake cupcakes

Who doesn’t love carrot cake?

But while carrot cake may seem healthy because it is made with a vegetable, traditional carrot cake is actually full of so much added sugar that you might as well be eating a Snickers bar.

With a soft texture and sweet carrot cake flavor, these low calorie carrot cake cupcakes offer you the best of both worlds.

They taste decadent enough for dessert yet are so healthy that you can even eat them for breakfast if you so desire.

And absolutely no one can ever tell they aren’t full of fat and calories!

Readers also love these Oreo Cupcakes

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (3)
Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (4)

The recipe can be oil free, egg free, dairy free, vegan, gluten free, high fiber, and added sugar free.

And each cupcake packs in close to 75% of the RDA for vitamin A.

Superfood carrots are a good source of beta carotene, promote healthy vision, and boost immunity from their high vitamin C content.

I like to add half a cup of raisins, or sometimes a handful of mini chocolate chips. These additions are optional.

The fancy 24 carrot cake cupcakes are great for brunch parties or served as a healthy Easter dessert or lunch box snack.

You may also like Sweet Potato Brownies

Step by step recipe video

Watch the video how to make healthy carrot cake cupcakes, above

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (5)

Vegan healthy carrot cake cupcake ingredients

Here’s what you will need to make your own carrot cake cupcakes.

Add carrots, flour, cinnamon, baking soda, salt, sugar of choice, applesauce or banana, optional oil, white or apple cider vinegar, and pure vanilla extract to the grocery list.

I like to use whole grain spelt flour for these healthy cupcakes. White flour, oat flour, and some brands of all purpose gluten free flour also work.

We have never tried the recipe with whole wheat flour or coconut flour. If you prefer to use almond flour, make these Gluten Free Carrot Cake Cupcakes.

For a fun flavor variation, swap out the applesauce for an equal amount of mashed banana, canned pumpkin puree, roasted sweet potato puree, or crushed pineapple. Or increase the protein by substituting regular or Greek yogurt.

The recipe works with regular sugar or unrefined coconut sugar or date sugar. Or go with granulated erythritol or xylitol for added sugar free carrot cake cupcakes.

While you can technically substitute a liquid sweetener, such as honey or pure maple syrup, the texture will be best with a granulated sweetener.

Vegetable oil or sunflower oil work well. If using coconut oil, melt it first and make sure none of the other ingredients are cold. For oil free cupcakes, sub an equal amount of additional applesauce, mashed bananas, or yogurt.

As for the carrots? You may use purple, yellow, or traditional orange carrots. Baby carrots and large carrots both work equally well.

Want more healthy cupcakes? Make Vegan Chocolate Cupcakes

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (6)

How to make the recipe

Line a cupcake tin with liners, and set the pan aside.

Peel and shred the carrots. The easiest way to shred carrots is in a food processor. You can also use a box grater.

Preheat your oven to 350 degrees Fahrenheit while you measure the ingredients.

In a large measuring cup or bowl, whisk together the shredded carrot, applesauce or banana, water, optional oil, vinegar, and pure vanilla extract.

Combine the flour, cinnamon, sugar, baking soda, salt, and optional raisins in a large mixing bowl. Stir the dry carrot cake cupcake ingredients very well.

Pour the wet ingredients into the dry, and stir until just evenly mixed. Do not overmix.

Divide the cupcake batter among the lined cupcake or muffin tins. The recipe should yield enough batter to fill a dozen standard size cups.

Or if you wish to make mini carrot cake cupcakes instead, portion the batter into lined or greased mini muffin tins.

Bake the pan on the center rack of the oven for twenty minutes if making large cupcakes or ten minutes for mini ones.

When time is up, a toothpick inserted into a domed cupcake’s center should come out mostly clean.

Enjoy plain or topped with any of the frosting options included below.

The cupcakes are even sweeter and fluffier the next day, and the liners should be easy to peel off after sitting overnight.

Store leftover cupcakes loosely covered on the counter for one or two days. If you still have leftovers after two days, it is best to cover and refrigerate for up to a week or freeze in an airtight covered container for up to three months.

The recipe was adapted from my Carrot Bread and Carrot Cake Muffins

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (7)

Healthy cream cheese frosting recipe

Feel free to eat the cupcakes unfrosted or topped with Coconut Butter.

This time, I chose to top them with a homemade cream cheese frosting. It can easily be both vegan and keto friendly, depending on the specific ingredients you choose. For a healthy option, choose unrefined coconut sugar and cashew butter over the butter.

Here is the recipe:

Bring eight ounces of cream cheese or vegan cream cheese to room temperature.

Use hand beaters or a stand mixer to whip the cream cheese with four ounces of butter or cashew butter an optional teaspoon of pure vanilla extract, and two cups of powdered sugar or coconut sugar.

You can also whip in a half teaspoon of ground cinnamon, a pinch of cardamom, the seeds of a vanilla bean, or the zest of one lemon if desired.

If the homemade cream cheese icing is too thick, slowly beat in a teaspoon of milk or water at a time, until it achieves your preferred thickness and texture.

Store any leftover frosting covered in the refrigerator for up to a week.

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (8)

You can also turn the recipe into a Healthy Carrot Cake.

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These healthy carrot cake cupcakes are moist, fluffy, and topped with thick vegan cream cheese frosting!

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (9)

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Print Recipe

Cook Time 20 minutes minutes

Total Time 20 minutes minutes

Yield 12 cupcakes

5 from 163 votes


  • 1 cup shredded carrot (200g)
  • 1/2 cup applesauce or yogurt
  • 1/3 cup oil or additional applesauce
  • 2 tsp pure vanilla extract
  • 2 tsp white or apple cider vinegar
  • 1 1/2 cups flour (For low carb, try this Keto Carrot Cake)
  • 1 tsp cinnamon
  • 3/4 tsp salt
  • 1/2 tsp baking soda
  • 1/2 cup sugar or coconut sugar or xylitol
  • 1/2 cup raisins (optional)


  • The carrot cake cupcake recipe works with spelt, white, or loosely packed Bob's all purpose gluten free flour.

    To make the cupcakes, preheat oven to 350F and place a dozen cupcake liners in a muffin tin. Combine all dry ingredients in a bowl, then set aside. In a large measuring cup, combine all liquid ingredients, including the carrot. Mix wet ingredients into dry, and immediately portion into the baking cups. Bake 20 minutes on the center rack of the oven. Allow the healthy cupcakes to cool before removing from the tray. The liners peel off easily after a day. If desire, frost with the healthy cream cheese frosting recipe above or with your favorite frosting.

    View Nutrition Facts


To turn the cupcakes into a cake, try this Vegan Carrot Cake Recipe.

Have you made this recipe?

Tag @chocolatecoveredkatie on Instagram

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (10)

More Healthy Dessert Ideas

Carrot Cake Banana Bread

Protein Cookie Dough

Chocolate Crinkle Cookies

Strawberry Mousse

Vegan Lemon Bread

My New Cookbook

Healthy Carrot Cake Cupcakes - Low Calorie Recipe! (2024)


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