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A close up of a mini carrot cake cheesecake cupcake, topped with whipped cream.
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5 from 1 vote


For the Carrot Cake Layer:

  • 1/4 cup granulated sugar
  • 1/4 cup brown sugar
  • 1/4 cup vegetable oil (or canola oil)
  • 1/4 cup applesauce
  • 1 egg
  • 1/2 tsp vanilla extract
  • 1/2 cup all purpose flour
  • 1/2 tsp baking powder
  • 1/4 tsp baking soda
  • 1/4 tsp salt
  • 1/2 tsp ground cinnamon
  • 1/8 tsp ground nutmeg
  • 1/2 cup shredded carrots

For the Cheesecake Layer:

  • 8 oz cream cheese (softened)
  • 6 TBS granulated sugar
  • 1/4 cup sour cream
  • 1 large egg
  • 1 tsp vanilla extract
  • 1 TBS all purpose flour
  • 1 pinch salt

Optional Toppings:

  • Whipped Cream
  • Ground Cinnamon


For the Carrot Cake Layer:

  • Preheat the oven to 350 degrees Fahrenheit. Line a muffin pan with paper liners, and set it aside.
  • In a medium sized bowl, add the sugars, oil, and applesauce and stir them together until combined.
  • Add in the eggs, and vanilla extract and stir them into the mixture.
  • Dump in the flour, baking powder, baking soda, cinnamon, and nutmeg. Stir them into the mixture.
  • Add in the grated carrot, and fold it into the batter. Set it aside till needed.

For the Cheesecake Layer:

  • In a medium sized bowl, beat the cream cheese until it's smooth.
  • Add in the sugar, and sour cream and mix in on medium speed until nice and smooth. Scrape the bottom and sides of the bowl as needed.
  • Stir in the egg and vanilla extract, until just combined.
  • Add in the flour, and salt, and lightly stir it into the mixture.

For Assembling the Cupcakes:

  • Scoop about 1.5 to 2 TBS of the carrot cake batter into the cupcake liners, dividing it evenly between them top.
  • Scoop about 2 TBS of the cheesecake mixture on top of the carrot cake mixture in the the cupcake liners.
  • Bake the cupcakes for 16 to 24 minutes, or until the sides of the cheesecake tops are set, and the center is just slightly jiggly.
  • Remove the pan from the oven and let the cheesecakes cool on the counter for one hour. Then transfer them to a refrigerator for at least one hour.
  • Top each cupcake with whipped cream, and a dash of cinnamon when serving, if desired.