A process and system for sterilization of a product pathway of a blow-fill-seal machine. The process comprises steps of: (1) isolating a holding tank from the product pathway; (2) supplying a sterilizing agent to the product pathway of the BFS machine when the holding tank is isolated; (3) stopping the supply of sterilizing agent to the product pathway when a threshold is reached; and (4) supplying filtered compressed air to the product pathway when the supply of sterilizing agent is stopped. The process is preferably executed automatically without human intervention once initiated. Also described is a system for carrying out the process including a processor, valves and temperature and/or pressure sensors which provide information to the processor to determine when to open and close the valves to supply sterilizing agent and/or compressed air to the product pathway or holding tank.