A process is disclosed for operating a PEM fuel cell system (2) with at least one PEM fuel cell module (4) equipped with a hydrogen H2 inlet valve (14) and an oxygen O2 inlet valve (18). In order to switch off the PEM fuel cell module (4), the oxygen O2 inlet valve (18) is closed during a first stage, and during a second stage the hydrogen H2 inlet valve (14) is closed while a predetermined partial oxygen O2 pressure is applied on a cathode part of the PEM fuel cell module (4). This measure ensures a reliable operation of the PEM fuel cell system (2).
