These Carrot Cake Cupcakes with Cream Cheese Frosting are a healthier version of a favorite dessert! They are made with whole grain flour and no refined sugar. You really CAN have a healthy cupcake with this recipe! 
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There are a million (maybe more!) carrot cake and carrot cake cupcake recipes on the Internet. You will have no trouble finding one if you look.
What there aren’t so many of are healthy carrot cake cupcake recipes . I know what you’re thinking, but having carrots in it doesn’t automatically qualify it as healthy. You know who you are. 😉
Most of the recipes for carrot cake cupcakes have the two main ingredients I prefer to avoid when baking as much as I can: white flour and refined sugar.
So I set out to make a healthier version of an old favorite. I used white whole wheat flour instead of regular old white and sweetened it with just a tinge of maple syrup.
These carrot cake cupcakes are definitely not overly sweet, but it works. Traditional cupcakes can be a bit much, so for me the sweetness level is perfect.
While I don’t usually shy away from fats, I decided not to use oil in these. My purpose was to keep the calorie count in check as I knew I was going to top my cupcake with cream cheese frosting. So unsweetened apple sauce stands in where the oil would be.
Even without the oil, these Carrot Cake Cupcakes are super moist. The texture is outstanding!
What about the cream cheese frosting?
You can’t have a carrot cake cupcake without cream cheese frosting. You just can’t. Don’t worry, I made the frosting healthier too! The maple-cinnamon cream cheese frosting I created for these cupcakes is amazing. Again I used maple syrup as my sweetener of choice and the result was fantastic.
Trust me, I love traditional cream cheese frosting with the 2+ cups of powdered sugar. I think that’s why I fell in love with carrot cake in the first place. But this maple syrup sweetened cream cheese frosting does the trick with a lot less sugar.
How many calories are in Carrot Cake Cupcakes?
Fair question. I looked at Food Network Magazines recipe for Carrot Cake Cupcakes with Cream Cheese Frosting and plugged in their ingredients to see the calorie count. It came to just about 500 calories for one frosted cupcake.
These healthier Carrot Cake Cupcakes are just 193 calories. BOOM.
This Carrot Cake Cupcake is one that I can feel good about the kids eating and would be perfect for a 1st birthday cake. I might even call this a legit breakfast. Go ahead; when your cupcake is healthy, you can eat it for breakfast!
How to Make Carrot Cake Cupcakes
If you try this recipe, please give it a star rating below. It’s so helpful for readers to see when a recipe is tried and true! I hope you love these Healthy Carrot Cake Cupcakes as much as we do!
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Healthy Carrot Cake Cupcakes with Cream Cheese Frosting
- Total Time: 45 minutes
- Yield: 12 cupcakes 1x
Description
So much healthier than traditional carrot cake, this light version of Carrot Cake Cupcakes are flavorful, moist, and always a hit!
Ingredients
For the Cupcakes
- 1 1/2 cups white whole wheat flour or whole wheat pastry flour
- 1 1/2 teaspoons baking powder
- 1/2 teaspoon baking soda
- 1 1/2 teaspoon cinnamon
- 1/2 teaspoon ground ginger
- 1/2 teaspoon ground nutmeg
- 3/4 teaspoon salt
- 2 eggs
- 2/3 cups unsweetened applesauce
- 1/3 cup maple syrup
- 2 teaspoon pure vanilla extract
- 1/4 cup crushed pineapple, drained
- 2 cups shredded carrots
For the Frosting
- 8 ounces organic cream cheese
- 4 tablespoons maple syrup
- 1 teaspoon pure vanilla extract
- 1 teaspoon cinnamon
Instructions
- Preheat the oven to 350 degrees. Line muffin tins with paper liners and spray with non-stick cooking spray or use silicone muffin molds *
- In a medium bowl, whisk together the flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt. Set aside.
- In a separate bowl, whisk together the eggs, applesauce, maple syrup, and vanilla. Stir in the pineapple and carrots.
- Combine the wet and the dry ingredients and stir until mixture is smooth.
- Spoon approximately 1/3 cup of the batter into each muffin liner. Bake for 22-25 minutes, until a toothpick comes out clean. Allow to cool on a rack before frosting.
- While cupcakes are cooling, prepare the frosting: In a medium bowl, beat together the cream cheese, maple syrup, vanilla and cinnamon until smooth and whipped.
- Frost your cupcakes once they are completely cooled. To frost your cupcakes, you can make them pretty by creating a make-shift pastry bag. Just snip the end of a plastic sandwich bag, put the frosting inside, and squeeze it out onto the cupcake. Easy! Enjoy!
Notes
*affiliate link
- Prep Time: 20 minutes
- Cook Time: 25 minutes
Nutrition
- Serving Size: 1 cupcake with frosting
- Calories: 193
- Sugar: 13.4 grams
- Fat: 7.8 grams
- Carbohydrates: 27.8 grams
- Protein: 4.5 grams
If you’re a big fan of carrot cake flavors, you’ll love some of my other carrot cake recipes! Check them out below and let me know if you try one!
Carrot Cake Energy Balls
Carrot Cake Oatmeal Muffins
Healthy No Bake Carrot Cake Bars
Carrot Cake Cookies
Carrot Cake Smoothie
This recipe was first published in 2011. A video was added March 2020.
hey, I absolutely love these cupcakes….they are divine! I was wondering if there could be frozen? I was considering making two batches and then freezing a few for next time? if it could be done like that,than how long could they be kept in the freezer and how do I defrost them (oven or at room temp?)
I think these would freeze great. My guess is they’ll keep for around 2-3 months in the freezer. I would defrost them at room temperature.
Im really hoping a get a quick response, from anyone please…. so i made these tonight and will be serving them for lunch tomorrow, should I put them in refrigerator? or keep them out? super thanks in advance!
I’m so sorry I didn’t see this last night. The cupcakes are fine stored at room temp, but because the cream cheese frosting doesn’t have a lot of sugar to preserve it, it needs to be refrigerated. I hope these were a hit for you! 🙂
I’m planning to make these for my son’s first birthday party! How many cupcakes does this recipe make? Thanks!
It makes 12 cupcakes!
I don’t have white whole wheat flour. I do have all purpose flour and whole wheat. Could I use one or the other of those, or a combo? Thanks!
I would do 50% all-purpose and 50% whole wheat. I hope you love these!
Hi this recipe sounds great. Definitely going on give it a try. Is the pinapple needed? Is there anything that would be an OK replacement. My son gets a rash everytime he eats pineapple? ?
I think you could just leave it out without a problem. Please let me know if you try it! 🙂
I tried this recipe and loved it!
So happy to hear that! Thanks for letting me know. 🙂
Carrot cup cakes r tasty.
how many calories are In these?
How many cupcakes and what size cupcakes does this recipe make?
It makes 12 standard size cupcakes.
I made these as written. I had to cook them a lot longer and they were still soggy. I would definitely skip the pineapple next time. These tasted like pineapple cupcakes, not carrot cake.
I have them in a warm oven right now to try and dry them out a little bit. I’m hoping the frosting will redeem them.
A good idea, but some changes need to be made to the recipe. Maybe adding nuts and skipping the pineapple would bring them closer to carrot cake.
Interesting. I’ve never had that problem nor have I ever felt the pineapple dominated. You didn’t add the pineapple juice with the pineapples, did you? I’m sorry these didn’t meet your expectations.
I found this receipe on Pinterest and was so excited to try it for our guests who are watching their diet. I like the fact it has some great healthly swaps! However, the frosting tasted very tart and the cupcakes did not have much flavor. I followed the receipe perfectly too. My husband and I are probably going to be the only ones eating them because we don’t want to throw them out.
I’m very sorry you didn’t enjoy these. They have always been well-received for us.
I made these yesterday and they are already gone! They are amazing and we all love the frosting!
So glad to hear it! 🙂
You don’t happen to know the calorie information on one of these delicious little suckers? Not including the frosting…just a standard cupcake size? These are amazing and my husband and kids even love them!!!
I just read some above comments and saw Katie posted the calorie count including the frosting….ummmmm 179 each? Not bad!
Not bad at all! 🙂
I just made the frosting and it is really good for my grandsons birthday party and the frosting is to runny to put in the cupcakes what am I to do any suggestions.
You could either add more cream cheese or try adding a little starch (either corn starch or arrowroot powder). I hope it works out for you! Happy birthday to your grandson!
*Update
These turned out great! They were not super sweet, as you said they wouldn’t be. So I made sure not to leave any sweetness out of the frosting – which was delicious.
I made the few changes to the recipe as I said I would, and they still turned out very good. (Used 1 cup of white AP flour and 1/2 cup of whole wheat flour, and used reduced fat cream cheese for the frosting.)
I made the cupcakes and the frosting the morning of, stored the cupcakes in airtight containers after they cooled down, and stuck the frosting separately in the fridge all afternoon to make sure it would stay firmer.
Everyone loved them! Even those “beef-eating men.” 🙂 Thanks for the recipe!
So glad to hear it! Thanks for letting me know. 🙂
These look and sound amazing!!
We are celebrating my little sister’s 16th birthday this weekend, and she has been trying really hard to lose weight so when she requested carrot cupcakes, I thought these would be the perfect fit for her to still have her birthday cake and eat it too.
I am thinking about using the same amount of flour, but changing it to 1/2 cup of whole wheat flour and 1 cup of white all purpose flour, since we have a few “beef-eating men” in the family that won’t want it to taste TOO healthy. So I’ll try to be a little sneaky here and still have that “healthyish” factor.
I also want to use 1/3 reduced fat cream cheese for the frosting, since that is what I have on hand. Hopefully the texture of the frosting doesn’t change too much.
I used on online calorie calculator, and these still came out to 179 calories each – frosting and all. That’s amazing! I’ll let you know how these turn out. Thanks for sharing!
Last Week was St. Patricks day, so my family decided they wanted carrot cupcakes with cream cheese frosting. I was going to use a classic carrot cake recipe that my family thinks is the best recipe ever, but…. Its made with one and a half cups oil, white flour, and TONS of sugar! The frosting has full fat cream cheese, tons of powdered sugar, and a bunch of butter.. I was annoyed because I was going to have to make these really unhealthy cupcakes that I would have to eat too. So I decided to do a sneak attack and find a healthier recipe for the cupcakes without telling anyone! I found this one and made them, and oh my gosh they thought I used the same recipe that I always use!!! I was so happy!! These were so moist and sweet, and I almost forgot they were healthy when I was eating my cupcake. Thanks so much for sharing this recipe!
I love that you didn’t tell them! This comment really made my night–thanks for letting me know you and your family enjoyed these. 🙂
Haven’t tried the cupcake part of the recipe but made the frosting. Simply Divine!!! I will use this as my main frosting recipe from now on. I even used it as a dip for apples….cant stop eating it.
Thanks for letting me know! 🙂
Hi, I may have missed it, but I can’t find what the yield is for this recipe. 12 or 24? Thanks!
This is just what I have been looking for! I will be making these for my 2yo to take to school for her birthday. And you are right..there are TONS of recipes for carrot cake but most of them are very far from being healthy. Thank you!
You’re welcome. Enjoy! 🙂