Preheat oven to 350 F. Place paper liners in a standard sized cupcake tin and set aside.
In a medium bowl, beat together cream cheese and sugar on medium speed until smooth, about 1 minute. Add eggs, vanilla and flour. Mix until light in color and texture, about 1 more minute. Scrape down the sides of the bowl if necessary. Set aside.
In a medium bowl, whisk together flour, baking powder, baking soda, salt, cinnamon and nutmeg. Set aside.
In the bowl of a stand mixer (or using a hand mixer), beat together granulated sugar, brown sugar and vegetable oil on medium speed until combined, about 1 minute. Add eggs and vanilla, and mix until incorporated, about 1 more minute. With the mixer on low, slowly add the flour mixture to the wet ingredients. Mix just until combined, about 15 seconds. Stir in the shredded carrots by hand.
To assemble, scoop one tablespoon of carrot cake batter into prepared cupcake liners. Top with two tablespoons of cheesecake mixture. Bake for 22 minutes or until the edges of the cheesecake are set and the centers are still slightly jiggly. Cool completely at room temperature, then refrigerate for at least 2 hours. Top with whipped cream and a dash of cinnamon. Serve chilled.