A method for controlling a vapour compression system (1) is disclosed. Malfunctioning of a gas bypass valve (8) is registered. An actual opening degree of the gas bypass valve (8) is derived, and a target opening degree of the gas bypass valve (8) is derived, based on one or more control parameters of the vapour compression system (1). The actual opening degree is compared to the target opening degree, and the vapour compression system (1) is controlled based on the comparison, and in order to match a mass flow of gaseous refrigerant through the gas bypass valve (8) to the actual opening degree of the gas bypass valve (8).