Preheat oven to 350 degrees F. Line two baking sheets with parchment paper; set aside.
In a medium bowl, whisk together the flour, sugar, baking soda, baking powder and salt; set aside.
In the bowl of an electric mixer, cream together the peanut butter, honey and shortening on medium speed until light and fluffy, about 3 minutes. Add the egg and vanilla and mix until combined. Reduce the mixer speed to low and gradually add the dry ingredients, mixing until just combined. Give the mixture a final stir with a rubber spatula to ensure all of the flour has been incorporated.
Use a medium cookie scoop (about 2 tablespoons of dough) to scoop out dough and roll into a ball between the palms of your hands. Roll in the sugar and place on the prepared baking sheets about two inches apart. Using fork tines, press a criss-cross pattern into the tops of the cookies, flattening them into disks.
Bake until lightly golden brown, about 10 to 12 minutes. Allow the cookies to cool on the baking sheet for 5 minutes, then use a spatula to remove them to a wire rack to cool completely. The cookies can be stored in an airtight container at room temperature for up to 5 days.