Preheat oven to 350° F. Line standard muffin tins with paper liners and set aside.
Sift together flours, baking powder, salt, cinnamon and nutmeg.
In the bowl of an electric mixer fitted with the paddle attachment, cream the butter and sugar together on medium-high speed until pale and fluffy. Add eggs, one at a time, beating until each is incorporated, scraping down sides of bowl as needed. Add vanilla and maple syrup. Reduce speed to low. Add flour mixture in three batches, alternating with two additions of milk, and beating until combined after each. Fold in the chopped pecans.
Divide the batter evenly between the prepared liners, filling each about ¾-full. Bake until a toothpick inserted in the center comes out clean, about 20 minutes, rotating the pans halfway through baking. Let cool in the pan about 5 to 10 minutes, then transfer to a wire rack to cool completely.
To make the frosting, in the bowl of an electric mixer fitted with the paddle attachment, beat the butter and cream cheese on medium speed for about 5 minutes. Turn the mixer down to low speed and gradually add in the confectioners’ sugar until incorporated. Add in the maple syrup and salt and mix until incorporated. Turn the mixer back up to medium-high speed and beat for an additional 2 to 3 minutes minutes, or until light and fluffy.
Pipe the frosting onto the cupcakes and sprinkle with chopped pecans. Enjoy!