Treat yourself to this classic recipe but with a healthy twist. These Healthy Carrot Cake Cupcakes use applesauce and pure maple syrup...making them naturally sweetened and extra moist!
Carrot cake is something special. Just saying the word brings to mind a yummy, flavorful dessert that stands alone. After all, what other cake can tastefully hold over a cup of carrots? Very impressive!
I enjoy carrot cake so much that I knew I just had to make a healthier version of it. This way, I (and the fam) can enjoy it way more often. Kinda like what I did with my Healthy Lemon Bars (with No Refined Sugar!).
With Greek yogurt frosting and healthy ingredients like spelt flour, walnuts, and ground ginger (it’s anti-inflammatory – did you know?), these tasty mini’s will quickly become your go-to healthy carrot cake recipe.
Ready to give it a whirl? Let’s make 'em!

Is Carrot Cake The Healthiest Cake?
Healthy Carrot Cake can easily be made into a healthy version – and that makes it a better choice than the average cake. How do we do that? We use healthy flour instead of refined white flour, coconut oil as opposed to an unhealthy oil, and Greek yogurt as a protein-rich ingredient (instead of processed sugar icing).
So, I’d say it’s a pretty healthy cake. And, on that note, I'd also say chocolate zucchini bread is another irresistible option….

How To Make These Cupcakes Healthy
These carrot cake cupcakes are healthy because I’ve taken out not-so-good ingredients like refined sugar and flour. Then I replaced them with extra good-for-you stuff. Here's how:
- Instead of butter and any trans fates, I made these cupcakes with coconut oil and unsweetened applesauce (be ready for moist and super-delicious cupcakes!).
- I replaced refined sugar and unhealthy sweeteners with maple syrup.
- Spelt flour is my choice over refined white flour. More on why I dislike refined flour.
- Full-fat Greek yogurt makes a yummy frosting that gives a little protein boost.

Ingredient Notes
These cupcakes are full of goodness yet decadent enough to let you know you are treating yourself - as you should on a regular basis! What do you need to make these delicious mini cakes of goodness?
- Spelt flour: Rather than using processed white flour, I use spelt flour. Baking made with spelt flour is still light and the taste is compatible with fruits (like blueberries) and veggies (like carrots). You can substitute it 1:1 as well.
- Pure maple syrup: Maple syrup is a great natural sweetener. It also contains antioxidants and nutrients like manganese and calcium.
- Unsweetened applesauce: Want to add fiber, vitamins, and a natural sweetener to your healthy carrot cake cupcakes? Use unsweetened applesauce. The recipe calls for ¼ cup which makes for a moist cupcake.
- Milk: Use any type of milk that suits you. I recommend almond, cashew, soy, or any other plant-based milk, and dairy milk is fine also.
- Plain Greek yogurt: A super-delicious frosting can be easily whipped up using full-fat Greek yogurt.

Ingredient Substitutes
- Applesauce: If you are out of applesauce, you can sub a ripe mashed banana instead.
- Milk: Those who cannot have lactose can choose plant-based milk. Almond or cashew work well.
- Greek yogurt: Like the milk, the yogurt can be switched for a plant-based version.
- Oil: I use coconut oil but you can use olive oil or sunflower oil instead.
- Flour: I prefer spelt flour for this recipe but suitable swaps are amaranth, barley, whole wheat, and rice flours.

How To Make Vegan
You'll just need to swap out the eggs for chia eggs to make these cupcakes vwgan. How to make a chia egg? Take 1 tablespoon of chia seeds and mix it with 2.5 tablespoons of water. Stir and let it rest for about 5 minutes. Now you’ve got your chia egg! Also, make sure you use vegan milk (like almond or coconut) for the milk portion of the recipe. As for the frosting, go with a plant-based yogurt.
How To Make The Greek Yogurt Icing
Using full-fat plain Greek yogurt is key to healthy icing for carrot cake. No sugar crash here! The frosting on these tasty cupcakes is made with 3 simple ingredients; Greek yogurt, pure maple syrup, and vanilla extract. this triple threat makes a frosting that is light and sweet, but not overpowering.

How To Store And Freeze
It’s best to store these delicious cupcakes in the fridge. Use an airtight container and keep them for up to 4 days. If you’d like to freeze them for another time, let them cool, place them in a reusable freezer bag, and freeze them for as long as 3 months.
Note: In this case, I add the frosting after – I don’t freeze them with the frosting on. I make it fresh when we eat them.
More Healthy Cupcakes and Muffins
So quick and easy to make and a delightful treat in a couple of bites—that’s the beauty of the cupcake. Try these other cupcake and muffin recipes if you agree!
- Sweet Zucchini Cupcakes With Cream Cheese Frosting
- 9 Ingredient Blender Chocolate Muffins
- Healthy Banana Chocolate Chip Muffins
- The Best Healthy Strawberry Muffins
- Healthy Carrot Cake Recipe

Healthy Carrot Cake Cupcakes
Equipment
- muffin tin
*This post may contain affiliate links for products I use often and highly recommend.
Ingredients
For the Wet Ingredients:
- ¾ cup milk, like almond or soy
- ¼ cup melted coconut oil, cooled
- 2 large eggs at room temperature
- ⅓ cup maple syrup
- ¼ cup unsweetened applesauce
- ½ teaspoon vanilla extract
- 1 ½ cups peeled, grated carrots (about ½ pound)
- 1 teaspoon orange zest
For the Dry Ingredients:
- 1 ½ cups spelt flour
- ⅓ cup raw walnuts, chopped
- 2 teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon ground cinnamon
- ½ teaspoon ground ginger
- ¼ teaspoon sea salt
For the Cupcake Frosting:
- 2 cup full-fat plain greek yogurt
- 4 tablespoon pure maple syrup
- 2 teaspoon vanilla extract
Instructions
- Preheat oven to 350 degrees F and spray non-stick 12 cupcake tin with cooking spray or line with cupcake liners.
- In a large mixing bowl, combine the coconut oil, eggs, pure maple syrup, applesauce, milk, vanilla extract, and orange zest. Stir to combine.
- In a separate mixing bowl, whisk together the flour, baking powder, baking soda, walnuts, cinnamon, ginger, and sea salt.
- Add the dry Ingredients into the wet mixture, and stir until smooth. The batter will resemble a cake-like batter consistency.
- Add the shredded carrots, and fold into the mixture.
- Divide batter into prepared cupcake tin (I use an ice cream scoop) and bake for 20 minutes, or until tops spring back to the touch or a toothpick inserted in the middle comes out clean.
- Remove from the oven and let cool completely.
- While cupcakes are baking, prepare the frosting. Stir together the Greek yogurt, pure maple syrup, and vanilla extract.
- Once the cupcakes are cooled, spread the frosting over the top of the cupcakes.
- To store, refrigerate in a glass airtight container for up to 4 days.
Nutrition
This post contains affiliate links for products I use regularly and highly recommend.



Rose Omar
Dear Lacey,
I love reading your page. It's clean, simple and recipes are great. I am glad that I stumbled upon your blog by chance.
Happy 1st Blogssary and keep the recipes coming.
Lacey Baier
Thank you so much, Rose. I really appreciate your feedback 🙂
Amanda
Thanks for posting this recipe, I made it this weekend for my mother-in-law's birthday (carrot cake is her favorite) and it was a big hit! It was such an easy recipe too, I will definitely be making this again.
Thanks again, Amanda
Maryam
Just stumbled across your page and glad I stopped by. Will try this recipe tonight and hope it's a hit as I am sending them off to Hubby's work in the morning.
Lacey Baier
I hope you all enjoy the cupcakes, Maryam!
itsmedani
The Cream Cheese Frosting...most recipes call for butter along with cream cheese. I see this one doesn't. Is there a reason before I try it? I would like to eliminate the butter if it will turn out well. I am making a large amount of carrot cake cupcakes and looking for good recipes.
Lacey Baier
Very good question! There was no particular reason for not including the butter for the frosting, but it has turned out fine every time I make it. 🙂
Lelah
I love that the frosting doesn't have butter in it, that way you can really taste the cream cheese flavor. It's delicious!
Lacey Baier
I agree! You really don't miss the butter. Shocking, but true 😉
Lelah
Question - do you think I could make this in a round cake pan instead of as cupcakes? Looking for a recipe for my birthday cake! Thanks.
Lacey Baier
Hi Lelah! Yes, you definitely can make this recipe in a cake form -- I've done it before 🙂
Just bake until the cake springs back in the center and a knife/toothpick inserted into the center comes out clean, about 30-40 minutes, depending on your cake pan size. Good luck! (and happy birthday!)
Lelah
I used a 9 inch cake pan and baked it for about 35 minutes. It turned out beautifully! Thanks.
Lacey Baier
Yay -- so glad it turned out well, Lelah!
Mogasaur
Hi there!
Great blog! I just made a batch of these carrot cake cupcakes and boy did turn out well!!! Super delicious recipe, not too heavy, but still a nice, moist carrot cake! Easy and flavorful without being over-spiced. Taking them to my co-workers tomorrow- I am sure they will be a success.
Cheers!
Lacey Baier
Yay -- a success! Glad you enjoyed them!
Sageist
Congrats on the anniversary. And great way to celebrate...the cupcakes look tasty.
Lacey Baier
Thank you very much!
Dustin Baier
Congrats! I know that you really worked hard to get to this point and I had to eat lots of good food 🙂
Lacey Baier
Thanks for all your support, Dustin -- couldn't have done any of this without you!
Jen at The Three Little Piglets
Congratulations on your blogiversary! That's so exciting for you!
Lacey Baier
It certainly is, Jen! 🙂
Conna
Happy anniversary with many returns !!!!
Thank you for blogging .... I really enjoy your posts !
Lacey Baier
Thanks so much, Conna. I'm so glad 🙂
NanaBread
Happy Anniversary, Lacey! The world is a better place because of your blog. Best wishes for many more years of blogging fun and a fabulous new pizza kitchen to come!
Lacey Baier
Thank you very much, Jeanne! You are so very kind -- what a nice thing to say!
Kate
Happy Blogversary, Lacy! I love your blog and can't wait to see what the next year brings!
Lacey Baier
Thank you so much, Kate! I really appreciate your support 🙂
Karen M
Happy Anniversary!!! What a great way to start it off.
Lacey Baier
Right?? 😉 Thanks, Karen!
Angelica
Happy Blogiversary!!! I've really been enjoying your blog and I wish you success and happiness in all your ventures. Can't wait to try this recipe, thanks for sharing!
Lacey Baier
Thanks so much, Angelica!
Miss Becky
congratulations on your one-year anniversary for your blog - just one of your many blessings. I don't recall now how I found you, or when, but I'm awfully glad I did! I am always on the look-out for a new carrot cake recipe and these cupcakes look like a must-do. have a great week Lacey.
Lacey Baier
Thanks so much, Miss Becky! I'm awfully glad you found me too 🙂 I always enjoy your comments and visits to my site. I hope you enjoy the carrot cake -- I'd love to know how it turns out!
David
Hello Lacey, I must say these Carrot Cup Cupcakes were absolutely delicious to say the least...Thank YOU 🙂 the only thing I did change was the frosting, I piped Pumpkin Spice cream cheese for the frosting....EXCELLENT!!!
Lacey Baier
So glad you enjoyed them, David. Pumpkin Spice cream cheese frosting sounds amazing.