In the bowl of a stand mixer fitted with the paddle attachment, beat butter, brown sugar, honey, molasses, salt, and cinnamon at medium speed until combined. In a small bowl, whisk together all-purpose flour and baking soda. Gradually add whole-wheat flour to butter mixture alternately with all-purpose flour mixture, beating until combined.

Roll dough to ⅛-inch thick 18x16-inch rectangle between 2 sheets of parchment paper. Transfer to a baking sheet. Remove top layer of paper, and score dough with a knife into 2-inch squares, being sure to cut all the way through. Use a wooden skewer to make holes in crackers. Freeze for 30 minutes.

Preheat oven to 350° F. Bake until crackers begin to brown, about 10 minutes. Once cooled, break apart into squares.