The bacteriostatic properties of carbon disulphide (CS₂) hamper its biodegradation in conventional biofilters. The response of four biofilters operating in downflow mode and reverse-flow mode was compared in a laboratory-scale plant treating CS₂ under sudden short-term changes in operating conditions. A process shutdown for 24 h, an inlet concentration increase and an interruption of the inlet air humidification for 48 h at an empty bed residence time (EBRT) of 240 s did not impact significantly on biodegradation performance, regardless of flow mode. Nevertheless, a reduction in the EBRT to 60 s resulted in a significant decrease in removal efficiency in all the biofilters. The CS₂ degradation profile showed that the reverse-flow mode strategy rendered a more homogenous distribution of biomass along the bed height. The benefits of the reverse-flow mode were demonstrated even when the unidirectional flow mode was re-established.