Preheat oven to 350 degrees Fahrenheit. Line a muffin pan with paper cupcake liners.
Whisk the flour, baking powder, baling soda, cinnamon, nutmeg and salt together in a bowl. Set aside.
Using and electric mixer with a paddle attachment or hand mixer, beat the butter and sugar together until light and fluffy. Beat in the eggs, one at a time until combined. Mix in the vanilla, then reduced apple cider until combined. Slowly stir in the flour mixture just until combined. the batter may have a few lumps. Fold in the chopped apples.
Fill the cupcake liners 3/4 full with batter. This recipe makes 14-16 cupcakes. Bake for 15-18 minutes (depends on your oven) until the tops puff and a toothpick inserted comes out clean.
Remove from oven and cool completely before frosting.