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Carrot Cake Cheesecake Cupcakes are an easy way of combining carrot cake and cheesecake! This easy cupcake recipe is the original cheesecake cupcake and is topped with a cream cheese frosting. Carrot Cake can fix anything. So can cheesecake. Together? They can run the world.

cupcakes with tan frosting on a cutting board.


Original Cheesecake Cupcake Recipe

I originally wrote this post back in 2012, can you believe that? Back then I didn’t know I was creating one of the most popular new recipes to hit the internet. I don’t know if it’s coincidence or not, but ever since I posted these cupcakes, carrot cake cheesecake cakes (and other versions of cheesecake cupcakes) have flooded the internet. I posted these before Pinterest even existed (I know, right? What was it like without Pinterest?!) I like to think I started a trend (like I did with peanut butter snickerdoodles) so I’m considering this cupcake recipe to be the ORIGINAL Carrot Cake Cheesecake Cupcake.

What is a cheesecake cupcake?

You might think of a cheesecake cupcake as a mini cheesecake with graham cracker crust, but that’s not what I think of. No – I make cheesecake cupcakes as cupcakes with cheesecake on top!

These cupcakes are my favorite carrot cake recipe with a cheesecake topping and cream cheese frosting!

How to make Cheesecake Cupcakes

  • Mix cheesecake in a medium bowl – you can use a hand mixer or a stand mixer fitted with the paddle attachment. Beat on medium-high speed until mixture is smooth.
  • Mix up the carrot cake cupcake batter.
  • Place cupcake batter in muffin pan lined with cupcake liners. Then spoon some of the cheesecake on top.
  • Bake until the cheesecake is set and a toothpick stuck in the cupcake part comes out clean. Cool to room temperature then chill at least 8 hours before serving or frosting.
cupcakes with tan frosting on a cutting board.

Variations

cupcakes with tan frosting on a cutting board.

Expert Tips

  • You can actually put this cheesecake on any of my cupcake recipes.
  • Please use real carrots that you shred yourself; don’t use pre-shredded carrots. They’re too thick to get soft in the cake.
  • Make sure your ingredients are room temperature to avoid lumps, even the egg. Otherwise your cheesecake will be lumpy!
  • The cheesecake will collapse a bit into the cupcake – fill the hole with more frosting!
  • This recipe makes 12 perfect cupcakes. If you want a bite size version, make MINI Cupcakes using mini muffin pans (it’ll make about 4 dozen).

FAQs

How do you know when cheesecake cupcakes are done?

The cheesecake will be puffed and no longer glossy and a toothpick will come out clean.

How do you store these cupcakes?

Store these cupcakes in the refrigerator. You can also put them in the freezer for up to 2 months. Then just thaw them when you want to grab one out of the freezer.

cupcakes with tan frosting on a cutting board.

Carrot Cake Cheesecake Cupcakes Recipe

5 from 23 votes
Carrot Cake Cheesecake Cupcakes are an easy way of combining carrot cake and cheesecake! This easy cupcake recipe is the original cheesecake cupcake and is topped with a cream cheese frosting.
Prep Time 30 minutes
Cook Time 20 minutes
Total Time 50 minutes
Yield 12 cupcakes
Serving Size 1 cupcake

Ingredients
 

For the Cupcakes:

  • 1 large egg
  • ¼ cup unsweetened applesauce
  • ¼ cup vegetable oil
  • ¼ cup packed brown sugar
  • ¼ cup granulated sugar
  • 1 teaspoon vanilla extract
  • ½ cup all purpose flour
  • ½ teaspoon baking soda
  • ½ teaspoon baking powder
  • ¼ teaspoon salt
  • ½ teaspoon cinnamon
  • ½ cup shredded carrots
  • ½ cup chopped pecans or walnuts optional

For the Cheesecake:

  • 1 8 ounce package cream cheese room temperature
  • 2 tablespoons sour cream room temperature
  • ¼ cup sugar
  • 1 teaspoon vanilla
  • 1 large egg room temperature

For the Cream Cheese Frosting:

  • 8 ounces cream cheese softened
  • ½ cup unsalted butter softened
  • 3 cups powdered sugar
  • 1 teaspoon vanilla extract
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Instructions

  • Preheat oven to 350°. Line muffin pan with liners. Set aside.
  • Make the cake batter: In a large bowl, beat together egg, applesauce, oil, sugars, and vanilla. Mix in flour, baking soda, baking powder, salt, and cinnamon. Stir in carrots and nuts, if using. Pour evenly into 12 muffin tins (about 2 tablespoons per cupcake). Set aside.
  • Make the cheesecake batter: make sure all ingredients are room temperature to avoid lumps. Mix together cream cheese, sour cream, egg, sugar, and vanilla with a hand-held mixer. Pour evenly on top of cake batter in muffin pan (about 1-2 tablespoons per cupcake).
  • Bake for about 18-25 minutes, until cheesecake is no longer runny. Cool completely. Chill at least 1 hour before serving. You can frost them once they’re room temperature, but don’t serve until they’ve chilled a bit so the cheesecake can set.
  • Make the frosting: Using a hand mixer, cream butter and cream cheese until fluffy. Slowly add in powdered sugar and vanilla. Mix until smooth. Frosting option: use a 1M tip for a beautiful cupcake. Store in refrigerator for up to 3 days or freeze unfrosted cupcakes for up to 1 month.

Recipe Video

Recipe Notes

  • Make sure your ingredients are room temperature to avoid lumps, even the egg. Otherwise your cheesecake will be lumpy!
  • The cheesecake will collapse a bit into the cupcake – fill the hole with more frosting!
  • This recipe makes 12 perfect Carrot Cake Cheesecake Cupcakes. If you want a bite size version, make MINI Carrot Cake Cheesecake Cupcakes using mini muffin pans (it’ll make about 4 dozen).

Recipe Nutrition

Serving: 1cupcake | Calories: 410kcal | Carbohydrates: 49g | Protein: 3g | Fat: 23g | Saturated Fat: 13g | Cholesterol: 77mg | Sodium: 177mg | Potassium: 105mg | Sugar: 43g | Vitamin A: 1445IU | Vitamin C: 0.3mg | Calcium: 44mg | Iron: 0.6mg
Nutritional information not guaranteed to be accurate
Course Dessert
Cuisine American

Favorite Carrot Cake Recipes

Last Updated on February 21, 2024



Dorothy Kern

Welcome to Crazy for Crust, where I share recipes that are sometimes crazy, often with a crust, and always served with a slice of life.

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44 Comments

  1. I made the carrot cake cheesecake for my family on Christmas Day, and everybody loved them. Thank you so much for the recipe, and can’t believe how easy it is to make.

    1. Yes you totally can! The amounts of cheesecake and cake batter might not be even (you may have extra cake batter) but it’ll work just fine!

  2. They taste wonderful!!! I am making them in advance for a birthday guy. He requested carrot cake but I wanted to take it up a notch. Thanks!

  3. Dearest Dorothy, I know I’m a bit late to the game here, seeing the dates on the comments above from 2012-2014, but I don’t care it has taken me two years to find this wonderfully amazing delicious dessert recipe. I am not a great baker but your recipe for carrot cheesecake cupcakes made me one tonight! The recipe was so easy to follow, baked up quickly and was so light, moist and amazingly tasty. Thank you for sharing your recipe. I’m excited to start following your blog.

    1. I’m so glad you enjoyed them Traci!! I love these cupcakes and they remind me I need to do other cheesecake cupcake versions!

  4. I’ve made the Carrot Cake Cheesecake Cupcakes a couple of times. They are my husbands favorite! I was wondering if you have ever tried putting the cheesecake on the bottom?

    1. Hello! I’m wondering if you did try to put cheesecake on bottom? I thought the same idea so I’m wondering before I make them. I wondered if the cake would sink into cheesecake if it was on bottom though. I thought with the carrot cake on top it would pair better with the cream cheese frosting?
      Thanks,
      Becky

  5. My niece made these for Easter and they were wonderful! Once I was home I was sorry I hadn’t taken a second one home with me. Only question I had was how finely to grate the carrots, and if it matters if I use a cheese grater or if a food processor is needed – thanks for sharing this great recipe!

    1. I use a regular box grater whenever I grate carrots! Less to clean than the food processor! But you can use either. 🙂

  6. LOVE this recipe!!! I made these cupcakes for a friend’s birthday last night. To say they were a hit is putting it lightly. These were quick and easy to make. 🙂

  7. Your presentation is really nice. I am planning to make the best cheesecake in New York by adding up a little something new on my original recipe. I haven’t tried carrots yet and I would liek to try it. Thank you for sharing this recipe.

  8. I made these for Easter and the cream cheese frosting is heavenly. It has become our go-to cream cheese frosting recipe. Rich and sinful. We’ve used it with a lemon cake and plan to use it for the red velvet cupcakes at a bridal shower this summer.