Preheat oven to 350 degrees Fahrenheit. Line two muffin tins with cupcake liners and set aside. Feel free to use patriotic paper liners or silicone ones.
Combine the flours, baking powder, salt, cinnamon, and nutmeg in a large measuring cup. Pour through a fine mesh sieve into a large mixing bowl.
In an electric mixer, or using a handheld mixer, cream the butter and sugar on a medium-high speed. When it's pale and fluffy, you've reached the right consistency.
Add the eggs one at a time, mixing well to incorporate each one before adding the next. Scrape the sides of the bowl as needed. Add the vanilla.
Reduce the mixing speed to low and add in the flour mixture in thirds. After each batch, add a third of the milk to the batter. Beat until combined after each addition, and continue the pattern until all flour and milk has been added.
Chop your Granny Smith apples finely, or process them in a food processor. You want them to retain shape so if you use a food processor, be sure they don't turn to mush.
Add the Granny Smith apples to the batter and stir to combine.
Fill the cupcake liners until they are each 3/4 full, giving the cupcakes room to rise. Bake for about 20 minutes, or until a toothpick inserted in the center comes away clean. Rotate the pans in the oven after the first 10 minutes.
Let cool in the pan for about 10 minutes. Transfer to a wire rack to cook completely.