Preheat oven to 350°F (175°C) and line a cupcake tin with liners. In a bowl, whisk together flour, baking powder, baking soda, cinnamon, nutmeg, and salt.
In another bowl, beat butter, brown sugar, and granulated sugar until light and fluffy. Add eggs one at a time, then mix in vanilla extract. Slowly add dry ingredients, alternating with buttermilk, until just combined. Fold in the chopped apples.
Divide batter evenly among cupcake liners, filling each about ⅔ full. Bake for 18-20 minutes or until a toothpick inserted in the center comes out clean. Let cool completely.
Beat cream cheese and butter until smooth. Gradually add powdered sugar, vanilla, and cinnamon. Frost cooled cupcakes and garnish with a sprinkle of cinnamon or apple slices.