A system for handling the sterilization of thin-body, pouch-type, flexible containers (1), provides for applying sacrificial closures (200) to the pouches, loading the provisional closed pouches to be sterilized on a transport device (300) for collective transport, to performing the sterilization of the transport device (300) carrying the provisional closed pouches and, finally, separating, in a sterile chamber, the sacrificial closures (200) from the pouches, performing filling and applying an inviolable cap (100).