A method of decontaminating an aseptic filling apparatus that includes stations including a content filling station arranged from an upstream side to a downstream side of a flow of a preform or container, and each of the stations is covered by a chamber. The method includes sterilizing the content filling station by performing a CIP and then an SIP or performing an SIP serving also as a CIP of the content filling station, removing a cleaning liquid used in the CIP or SIP, and performing a COP and/or an SOP of the various kinds of stations in a predetermined order. A first SOP using a first sterilizer and a second SOP using a second sterilizer are performed stepwise on the various kinds of stations while the CIP and the SIP or the SIP serving also as the CIP are being performed on the content filling station.