Abstract: The present disclosure relates to a method of controlling a steam sterilizer system comprising a boiler in which liquid water is turned into steam. Water is pumped from a container and the pumped water is passed through a degassing filter located upstream of the boiler in order to remove non-condensable gases (NCGs) dissolved in the water. The water is recirculated through the degassing filter for additional removal of NCGs, while water is prevented from flowing from the degassing filter to the boiler. Subsequently to recirculating the water through the degassing filter, at least a portion of the water is passed to the boiler. The present disclosure also relates to a control unit for performing the steps of the method, and to a steam sterilizing system comprising such a control unit.