A method for operating a compressor unit (2) comprising one or more compressors (8, 9, 10) is disclosed, the compressor unit (2) being arranged in a vapour compression system (1). Two or more options for distributing the available compressor capacity of the compressor unit (2) between being connected to a high pressure suction line (11) and to a medium pressure suction line (13) are defined. For each option, an expected impact on one or more operating parameters of the vapour compression system (1), resulting from distributing the available compressor capacity according to the option, is predicted. An option is selected, based on the predicted expected impact for the options, and based on current operating demands of the vapour compression system (1), and the available compressor capacity is distributed according to the selected option, e.g. by means of settings of one or more valve arrangements (14, 15).