Heat the oven to 350° F. Add cupcake liners to a 12-serving cupcake pans and set aside.
In a small bowl, melt the butter in the microwave, then set aside to cool. Alternately, melt the butter in a small saucepan on the stove.
Using the large holes of a box grater, grate the peeled and cored apples. Note: the apple will most likely turn brown from oxidation. This does not affect the taste or use.
In a medium-sized bowl, whisk together the flour baking powder, baking soda, salt, spices, and brown sugar.
In a large bowl, whisk the eggs, the cooled melted butter, vanilla, and greek yogurt until well combined.
Add dry ingredients to the bowl of wet ingredients and stir until well incorporated.
Stir in the shredded apples with a spoon. You should now have a nice thick batter.
Scoop ¼ cup of batter in the prepared cupcake liners, they should be ¾ full. Bake for 15-20 min or until a toothpick inserted in the center of a cupcake comes out clean. Let cool.