A system of managing the sterilisation of empty flexible pouches (1) provides applying sacrificial closures (200) to the empty pouches, loading the empty provisional closed pouches to be sterilised on a transport device (300) for the collective transportation, performing the sterilisation of the transport device (300) carrying the empty provisional closed pouches, and finally separating, in a sterile chamber, the sacrificial closures (200) from the pouches, filling and applying a tamper-proof cap (100).
