Preheat the oven to 375˚F. Lightly spray a baking sheet, and set aside.
In a medium bowl, mix together the flour, pretzels, baking soda and salt.
In a separate bowl, cream together the sugar, peanut butter, shortening, milk and vanilla until fully combined. Add in the egg, and beat until fully incorporated.
Slowly mix in the dry ingredients to the wet ingredients until fully combined. Fold in the chocolate chips.
Using a medium cookie scoop, scoop the batter onto the prepared baking sheet, around an 2 inches apart. Flatten them out with a fork to make a criss-ross pattern.
Bake in the preheated oven for about 8-10 minutes, or until the edges are beginning to brown. Remove from the oven, and let cool for around 2 minutes, and transfer to wire racks to cool completely.