Healthy Carrot Cake Cupcakes | With Sweet Greek Yogurt Frosting

Treat yourself to a decadent dessert with a kick of vitamin A (thanks carrots)! This post will show you how to make my healthy carrot cake cupcake recipe. It uses applesauce and maple syrup…making them naturally sweetened and extra moist!

Looking for a can’t resist, delicious cupcake recipe? You’ve found it! This healthy carrot cake cupcake recipe contains applesauce and maple syrup, making them naturally sweetened and extra moist. You’re going to love them!

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.

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!

Overhead view of ingredients for Healthy Carrot Cake Cupcakes, including shredded carrots, spelt flour, spices, walnuts, and maple syrup.

Is Carrot Cake The Healthiest Cake?

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. But chocolate zucchini bread is another irresistible option….

Overhead view of a glass bowl with a spatula in it, ready to mix the dry ingredients into the wet for Healthy Carrot Cake Cupcakes.

How To Make Carrot Cake 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:

Overhead view of cupcake tins filled with Healthy Carrot Cake Cupcakes batter.

Everything You Need To Make Carrot Cake Cupcakes

These cupcakes are full of nutrition 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, use spelt flour as a healthier choice. 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 healthy 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.
  • Shredded carrots: I like to add 1 ½ cups of washed, shredded carrots. Getting a little extra vitamin A (from beta carotene) in such a yummy way is awesome in my books!
  • 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.
  • Eggs: Another healthy ingredient in this recipe is eggs. Eggs provide protein and they help to bind the ingredients, too.
  • Spices: Cinnamon and ginger, along with sea salt, are the perfect spice combo for healthy carrot cake cupcakes.
  • Plain Greek yogurt: A super-delicious frosting can be easily whipped up using full-fat Greek yogurt.
Overhead view of 12 baked Healthy Carrot Cake Cupcakes cooling on a wire rack.

Ingredient Substitutes For Healthy Carrot Cake Cupcakes

  • 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.
Overhead view of a white bowl with ingredients for the cupcakes frosting, including Greek yogurt, maple syrup and vanilla extract.

Can I Make Healthy Carrot Cake Cupcakes Vegan?

It is possible to make carrot cake vegan, yes! You’ll just need to swap out the eggs for chia eggs. How to make a chia egg? It’s as simple as can be. 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 Healthy Icing For Carrot Cake Cupcakes

Using full-fat plain Greek yogurt is key to healthy icing for carrot cake. No sugary 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.

Close up side view of a Healthy Carrot Cake Cupcake iced and ready to eat, on a white plate, with other cupcakes in the background.

How To Store And Freeze Healthy Carrot Cake Cupcakes

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.

Overhead view of cooling Healthy Strawberry Muffins, with strawberry slices around the cooling rack.

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!

5 from 1 vote
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Healthy Carrot Cake Cupcakes
Prep Time
15 mins
Cook Time
20 mins
Total Time
35 mins

Looking for a can’t resist, delicious cupcake recipe? You’ve found it! This healthy carrot cake cupcake recipe contains applesauce and maple syrup, making them naturally sweetened and extra moist. You’re going to love them!

Categories: Sweet
Difficulty: Easy
Keyword: carrot cake cupcakes
Servings: 12 cupcakes
Calories: 166 kcal
Author: Lacey Baier of A Sweet Pea Chef
For the Wet Ingredients:
  • 3/4 cup milk, like almond or soy
  • 1/4 cup melted coconut oil, cooled
  • 2 large eggs at room temperature
  • 1/3 cup maple syrup
  • 1/4 cup unsweetened applesauce
  • 1/2 tsp vanilla extract
  • 1 1/2 cups peeled, grated carrots (about 1/2 pound)
  • 1 tsp orange zest
For the Dry Ingredients:
  • 1 1/2 cups spelt flour
  • 1/3 cup raw walnuts, chopped
  • 2 tsp baking powder
  • 1/2 tsp baking soda
  • 1/2 tsp ground cinnamon
  • 1/2 tsp ground ginger
  • 1/4 tsp sea salt
For the Cupcake Frosting:
  • 2 cup full-fat plain greek yogurt
  • 4 tbsp pure maple syrup
  • 2 tsp vanilla extract
  1. Preheat oven to 350 degrees F and spray non-stick 12 cupcake tin with cooking spray or line with cupcake liners.

  2. In a large mixing bowl, combine the coconut oil, eggs, pure maple syrup, applesauce, milk, vanilla extract, and orange zest. Stir to combine.

  3. In a separate mixing bowl, whisk together the flour, baking powder, baking soda, walnuts, cinnamon, ginger, and sea salt.

  4. Add the dry Ingredients into the wet mixture, and stir until smooth. The batter will resemble a cake-like batter consistency.
  5. Add the shredded carrots, and fold into the mixture.

  6. 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.

  7. Remove from the oven and let cool completely.
  8. While cupcakes are baking, prepare the frosting. Stir together the Greek yogurt, pure maple syrup, and vanilla extract.

  9. Once the cupcakes are cooled, spread the frosting over the top of the cupcakes.
  10. To store, refrigerate in a glass airtight container for up to 4 days.
Nutrition Facts
Healthy Carrot Cake Cupcakes
Amount Per Serving (1 cupcake)
Calories 166 Calories from Fat 63
% Daily Value*
Fat 7g11%
Saturated Fat 4g20%
Cholesterol 24mg8%
Sodium 119mg5%
Potassium 228mg7%
Carbohydrates 21g7%
Fiber 3g12%
Sugar 9g10%
Protein 5g10%
Vitamin A 5380IU108%
Vitamin C 2mg2%
Calcium 69mg7%
Iron 1mg6%
* Percent Daily Values are based on a 2000 calorie diet.

This post contains affiliate links for products I use regularly and highly recommend.

Lacey Baier

Hey there! I’m Lacey Baier and I’d like to welcome you! I’m a healthy lifestyle influencer and the creator of this clean-eating blog and YouTube channel, as well as cleanish, my clean-eating supplement brand. My recipes have been published on Food Network, Good Morning America, FoxNews, Tastemade, Fitness Magazine, and much more. I live in Austin, Texas with my husband and four kiddos. Let’s get started!

48 thoughts on “Healthy Carrot Cake Cupcakes | With Sweet Greek Yogurt Frosting

  1. Do you still have the recipe for the cream cheese icing that was originally in this post? I used to make these and loved them!

    1. I think maybe it’s the same as here? https://www.asweetpeachef.com/sweet-zucchini-cupcakes-with-cream-cheese-frosting/

      I was looking for a the same thing lol! I’ve made these with the cream cheese frosting in the past and they were amazingggg. I can’t tell if the carrot cake part of the recipe has changed too since the original one. I don’t remember the coconut oil but I may have just substituted it at the time hmm.

  2. These cupcakes are so good! But, then again everything you make is fantastic. Thank you for all of your wonderful recipes.

  3. This recipe was so great!! My sister and i made these for my dad’s 41st birthday and we’ve made them 3 times since the beginning of January. Thanks so much!!

  4. I was looking for a recipe online to make these cupcakes. I came across your recipe. I smell them baking in the oven. I can’t wait to try them.

  5. Hi Lacey! I was searching the internet for a carrot cake cupcake recipe and I found your website! I am so excited…I have been looking at your recipes for the last hour! Plan on trying many of them…This one first for my husband’s birthday! I will let you know what we think!

  6. last week my husband hinted that he would really like carrot cake muffins with cream cheese frosting. having never made these before, i searched the internet for a recipe and found yours. while he was out ice fishing, i made them yesterday in a snap. imagine his surprise when he saw them on the counter. he ate one and announced “my god. these are by far the best thing you’ve ever made!” guess he likes them. 🙂 thanks for an awesome recipe!!

  7. Hello, Just wanted to let you know, my youngest is also named Savannah and will be 1 yr old on Friday. I’m going to make these cupcakes for her birthday!

  8. 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.

  9. 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

  10. 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.

  11. 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.

      1. I love that the frosting doesn’t have butter in it, that way you can really taste the cream cheese flavor. It’s delicious!

  12. 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.

    1. 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!)

  13. 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.


  14. Happy anniversary with many returns !!!!

    Thank you for blogging …. I really enjoy your posts !

  15. 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!

  16. 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!

  17. 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.

    1. 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!

    2. 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!!!

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