Preheat the oven to 350 degrees F. Line muffin tray with liners.
Sift together graham flour, all purpose flour, baking powder, salt, cinnamon and allspice together. Set aside.
In the the bowl of a stand mixer fitted with a paddle attachment, cream butter, sugar, and honey on high speed until light and creamy. Turn the speed down and add the vanilla and eggs, one at a time, occasionally scraping down the sides of the bowl.
Slowly add the sifted dry ingredients to the butter mixture on low speed. Mix until just combined. Add the chocolate chips and mix until combined.
Divide the batter into the lined muffin pan, about 1/3 cup in each. Bake until tops are golden brown and a toothpick comes out clean, about 20-25 minutes. Cool the cupcakes on a rack while you prepare the frosting.