The invention relates to a method and a system for adjusting S/Na-balance of a sulphate pulp mill, wherein a pulp mill CNCG stream containing sulphur compounds is first scrubbed with an aqueous scrubbing solution containing an alkaline agent, thereby producing an aqueous spent scrubbing solution containing sulphides, which is then oxidized in a bioreactor by means of sulphur-oxidizing microbes, thereby obtaining an aqueous suspension containing elemental sulphur from which the elemental sulphur can be separated as a precipitate and the residual solution may be used for replenishing the aqueous scrubbing solution.