Preheat oven to 350° F. Line standard muffin tins with paper liners and set aside.
Sift together flours, baking powder, salt and cinnamon.
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 mix. Reduce speed to low. Add flour mixture in three batches, alternating with two additions of milk, and beating until combined after each.
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 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 vanilla and salt and mix until incorporated. Turn the mixer back up to medium-high speed and beat for an additional 4 minutes, or until light and fluffy. Fold in the orange zest.
Use a knife to cut out a small portion of the center of the cupcake. Fill the holes of the cupcakes with about 1 teaspoon of the pomegranate spread. Pipe the frosting onto the top of each cupcake. Garnish with pomegranate arils and enjoy!