Preheat your oven to 400 degrees. Line a muffin pan with cupcake liners.
In a small bowl, whisk together flour, baking powder, baking soda, salt, cinnamon and nutmeg.
In a large mixing bowl, add in the oil, sugar, eggs, and vanilla extract. Beat with a hand mixer on medium until combined.
Once your wet ingredients are incorporated, slowly add ⅓ of the dry ingredients. Beat until the dry ingredients are worked in. Repeat with the last to thirds of the dry ingredients.
Once the ingredients are well-combined, fold in the shredded carrots.
Scoop the batter into your muffin pan and fill ¾ full.
Bake for about 20 minutes or until a toothpick comes out clean when inserted in the center of the cupcake. Allow to cool completely.
Frosting
In a mixing bowl, add in the cream cheese and butter. Mix until light and fluffy.
Add in the powdered sugar and heavy cream. Mix until incorporated. Turn the mixer on high and beat for another 2 minutes until the frosting is fluffy.
Add the frosting into a piping bag with a 1A tip and pipe swirls on the cooled cupcakes.
Toppers
Divide your orange fondant into 10 1-inch balls.
Roll out each ball into a 2-inch long shape and ½ an inch thick. It should resemble a baby carrot.
Flatten the top of your fondant carrot where the leaves will go. Work the other end with your fingers to give to taper it off and give it a sort of point.
Use a toothpick to score some lines on the fondant carrot. This will give it some realistic texture. Place a fondant carrot on top of each frosted cupcake.
Color about ¼ cup of the leftover frosting with leaf green gel food color. Place in a piping bag fitted with a small round piping tip. Add 3 green leaves to the top of each carrot.