A method for controlling a vapour compression system (1) is disclosed. The vapour compression system (1) comprises an ejector (6) and a liquid separating device (10) arranged in a suction line. At least one evaporator (9) is allowed to be operated in a flooded state. A flow rate of refrigerant from the liquid separating device (10) to the secondary inlet (15) of the ejector (6) is detected, and it is determined whether or not the flow rate is sufficient to remove liquid refrigerant produced by the evaporator(s) (9) being allowed to be operated in a flooded state from the liquid separating device (10). In the case that it is determined that the flow rate of refrigerant from the liquid separating device (10) to the secondary inlet (15) of the ejector (6) is insufficient to remove liquid refrigerant produced by the evaporator(s) (9), the flow rate of refrigerant from the liquid separating device (10) to the secondary inlet (15) of the ejector (6) is increased, and/or a flow rate of liquid refrigerant from the evaporator(s) (9) to the liquid separating device (10) is decreased.