Prep Your Oven: Preheat your oven to 350°F (175°C) and line a 12-cup muffin pan with cupcake liners.
Combine Dry Ingredients: In a large bowl, whisk together the flour, cinnamon, cloves, nutmeg, ginger, baking powder, baking soda, and salt.
Mix Wet Ingredients: In a separate bowl, whisk the brown sugar, eggs, sour cream, vanilla, and oil until everything is smooth.
Make the Batter: Pour the wet ingredients into the dry ingredients and mix until just combined. Gently fold in the grated carrots and coconut flakes.
Fill and Bake: Divide the batter evenly among the cupcake liners, filling them about two-thirds full. Bake for 18-20 minutes, or until a toothpick comes out clean.
Cool Completely: Let the cupcakes cool in the pan for a few minutes before moving them to a wire rack to cool completely.
Whip the Frosting: In a bowl, beat the room-temperature cream cheese and butter until smooth. Slowly add the powdered sugar and vanilla, and beat until light and fluffy.
Frost and Serve: Once the cupcakes are totally cool, frost them generously and enjoy!