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.
Hi!! Thank you for sharing this recipe- it looks absolutely delicious! I want to make as a layer cake. Question: Do you think the frosting will work for a layer cake? Thank you again!
We loved these cupcakes but found that they stuck to the wrappers! Have you ever had that problem? Any suggestions?
Did you let them cool before trying to remove them? That tends to help. You can also spray the wrappers with cooking spray, which helps, too.
I left out the pineapple because I didn’t have any, and added some raisins & chopped nuts. It was easy and delicious!
Loved this… didn’t use icing .. was looking for a healthy muffin.. to eat in the am.. I did add plumped raisins.. they did stick to my muffin holders… will get spray next time..
This recipe was AMAZING! I’m not much of a baker, recipes always flop, but these were so simple…and best of all DELICIOUS! We’re not fans of wheat flour, so I did substitute with white flour but otherwise kept everything the same. Making these again this weekend for my son’s “some bunny is turning one” birthday.
Hello! I plan on making this into a one layer cake- would the frosting spread nicely on a cake? Or would it not be the right consistency for spreading on a cake?
Thanks!
Our family’s favorite! So healthy! I added raisins in our carrot cupcakes. I can eat it without frosting! So delicious! Not too sweet!! I’ve made it like 5 times so far. I made another batch for Easter!
I’m so happy to hear this Leah!
These turned out terrible. I followed the recipe exactly with no substitutions but they taste acidic and metallic, like there’s too much baking powder. They’re also very dry and bready, none of the sweetness from the fruit seems to have come through. I couldn’t get the cream cheese frosting to work either, I whisked it for at least 10 minutes but it never stopped being little lumps of cheese sitting in maple syrup. Honestly, even if I’d managed to get it to whisk the frosting didn’t taste that great either. Avoid this recipe, there’s so many other carrot cake recipes out there that would be an improvement on this one.
Hey Fiona,
Well, shoot. I’m sorry these didn’t turn out to your liking. I’ve had great luck with this recipe over the years and have gotten great feedback from other readers as well. I can’t imagine how cream cheese + maple syrup wouldn’t taste good together no matter what, but everyone has different taste buds, that’s for sure! I’ve also never had a problem getting my cream cheese to whisk together. Honestly, it sounds like your cream cheese was bad. :0 Thanks for your feedback and I’m sorry again that you didn’t enjoy my recipe.
Best,
Maryea
I had a quick question… is there a way to make this without the carrots and pineapple?
Maybe substitute apples or bananas?
Also.. is it possible to use homemade unsweetened apple butter vs applesauce?
I think shredded apples and bananas would work in place of the carrots and pineapple, the flavor will just be different. And apple butter should work instead of apple sauce, also.
Excited to try! Could I leave out the pineapple without ruining the chemistry? Also, going to use neufchatel cheese instead of cream cheese to make it even healthier!
I *think* it would be just fine to leave it out. Please let me know how it goes!
Just made these this morning for the first time. Haven’t made the frosting yet. They haven’t even cooled yet. 🙂 The carrots seem really prominent. I think next time I will grate them on the smaller side of the box grater. I also think I will increase the amounts of the spices next time. Thanks for a healthier baked treat recipe!
The frosting turned out a bit goopy for me, but 1/2 cup of powdered sugar is all it took to make it perfect. I know it defeats the purpose a little given that they’re meant to be healthy, but thought I’d mention it!
Thanks for the feedback! Yes, the frosting is not as firm as traditional frosting, but I’m glad you could get it to your liking with just a little powdered sugar. 🙂
Can these cupcakes be frozen (without frosting)? Can the frosting be frozen in a ziplock bag?
Yes, you can freeze the cupcakes. I have not tried freezing the frosting. Let me know if you try it!
I followed the recipe exactly as written but the batter turned out really dry. What is the consistency of this batter supposed to look or feel like? The frosting, on the other hand, was perfect!