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In a bowl, whisk together the all-purpose flour, whole-wheat flour, salt, baking soda, and cinnamon.
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In the bowl of an electric mixer fitted with the paddle attachment, combine the butter, dark brown sugar, granulated sugar, and honey. Mix on medium speed until well combined, about 1 minute. In two additions, add the dry ingredients, letting the first fully incorporate before you add the second.
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Turn the dough out and flatten it into a rectangular shape, wrap it tightly in plastic wrap, and refrigerate until chilled, about 30 minutes or up to 2 days. (The dough can be frozen, well wrapped, for up to 1 month.)
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Preheat the oven to 350 F. Line two baking sheets with parchment paper.
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Unwrap the chilled dough, and on a lightly floured surface, roll it out into a rectangle about â…› inch thick. Using a ruler and a pastry cutter or a sharp knife, cut the dough into 3-by-3-inch squares; use a spatula to transfer the rectangles to the prepared baking sheets as you go. Reroll the scraps of dough once, and cut out more cookies. Using a paring kninfe, gently score each square to create a line down the middle, taking care not to cut all the way through the dough. Using a fork, pierce each rectangle with two rows of six to eight marks.
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Bake the graham crackers, rotating the baking sheets halfway through, until they are golden brown, 15 to 20 minutes. Cool on a wire rack.
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The graham crackers will keep in an airtight container at room temperature for up to 1 week.