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

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
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
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
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 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.
You can also turn the recipe into a Healthy Carrot Cake.
Healthy Carrot Cake Cupcakes
Ingredients
- 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)
Instructions
- 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
Notes
Have you made this recipe?
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Ellerie says
Hi! Attempting to make a refined sugar free version… Could the applesauce be replaced with nonfat (Fage) greek yogurt, and the sugar with maple syrup? Would any of the other measurements need to be modified if so?
Thanks 🙂
Teresa Corrigan says
Great muffins. I subbed the applesauce for oil. They are good. But stick to the muffin papers. Maybe spray oil the muffin papers next time? Thank you for the recipe!
CCK Media Team says
Hi! You can also wait a day and the liners should peel off easily the second day. Let me know if that doesn’t work for some reason!
Doe acker says
No eggs in the loaf or muffins?
CCK Media Team says
Nope 🙂
Cindy says
These carrot cake cupcakes were so delicious!! I made them for my family for Easter and everyone loved them! I used granular Swerve for the cake batter and used confectioners Swerve for the icing. I used your Keto cream cheese frosting recipe. Thank you!
CCK Media Team says
Thank you so much for making them!
Kathleen Carullo says
I love this recipe!! I double it and have made it as a cake, muffins and even a loaf! So delicious!!! Thank you so much for sharing!
CCK Media Team says
Thank you so much for trying it 🙂
Dawn says
Can I substitute applesauce with yogurt?
CCK Media Team says
Yes!
Rachel Gibson says
I’m not a fan of applesauce, could I sub this for something else?
Rhonda says
I did see that the recipe calls for both applesauce, so just to confirm, if I don’t use oil, it would work just fine to use a LOT of applesauce: 1/3 cup plus 1/2 cup?
CCK Media Team says
We haven’t tried it so cannot vouch for it, but many readers have said yes it works!
Lauren says
These carrot cake cupcakes were delish!
Kirsten says
Baked these on Monday and was suitably impressed, the only difference I made was I used
Lupin Flour
Finely chopped date instead of raisins
Coconut sugar instead of xylitol
1 teaspoon blackstrap molasses
1/2 teaspoon ginger powder
1/8 teaspoon clove powder. Gave them an awesome flavour.
Will be making them again soon.
Angela says
Do I have to spray the cupcake liners?
CCK Media Team says
Nope 🙂
Sue says
I love this recipe exactly as it is and have made it several times now. I would like to sometimes add an egg to it for when we want muffins for a quick breakfast. How would you suggest I change the dry ingredients to accommodate the egg?
CCK Media Team says
Hi sorry we have never tried so really do not know. Have fun experimenting!
Joyce Shavers says
I love this recipe and frequently make it. I put them in the freezer and take out one at a time for a healthier decadent breakfast or dessert. I put a little oil in my cupcake tin and they pop out just fine without using liners.
Roseanne Morgan-Hulen says
Can you use oat flour, or almond flour in this recipe?
Roselyn Eichmann says
Your blog is a breath of fresh air. Thank you for sharing your wisdom with us.
Maria says
Hello- I am looking for the measurement for the WATER ingredient. I am not able to find it anywhere one the pages. I would appreciate the cup measurement for the water if indeed there is water…
It says “… whisk together the shredded carrot, applesauce or banana, water, optional oil, vinegar, and pure vanilla extract. Thank You.