Start by collecting all the ingredients. This will make the process flow smoothly. Make sure everything is at room temperature, especially the butter.
In a large bowl, combine the all-purpose flour, whole wheat pastry flour, baking soda, cinnamon, nutmeg, and sea salt. Whisk these dry ingredients to ensure even distribution.
In a separate bowl, cream the softened butter, dark brown sugar, honey, blackstrap molasses, and pure vanilla bean paste. Beat until the mixture is light and fluffy. Gradually add the dry flour mixture into the bowl, mixing until a dough forms.
Shape the dough into a disk, wrap it in plastic wrap, and place it in the refrigerator. Chill for at least 30 minutes. This step is key for better texture and handling.
Preheat your oven to 350°F (175°C). Dust your work surface with flour. Roll out the chilled dough to about 1/8-inch thickness. Using a sharp knife or cookie cutter, cut into squares or any desired shapes.
Place the cut crackers onto parchment-lined baking sheets. Sprinkle the cinnamon sugar blend generously over the top. Bake for about 10-12 minutes until the edges are lightly golden.
Remove from the oven and allow the crackers to cool completely on a wire rack. Once cooled, they become crispy and delicious. Enjoy with your favorite dips and spreads or simply on their own.