A multi-compartment transport refrigeration system comprising: a compressor having a suction port and a discharge port, the compressor suction port coupled to a compressor inlet path; a heat rejecting heat exchanger downstream of the compressor discharge port; a first evaporator expansion device downstream of the heat rejecting heat exchanger; a first evaporator having an first evaporator inlet coupled to the first evaporator expansion device and a first evaporator outlet coupled to the compressor inlet path, the first evaporator for cooling a first compartment of a container; a second evaporator expansion device downstream of the heat rejecting heat exchanger; a second evaporator having a second evaporator inlet coupled to the second evaporator expansion device and a second evaporator outlet coupled to the compressor inlet path, the second evaporator for cooling a second compartment of the container; a controller; a first evaporator outlet temperature sensor and first evaporator outlet pressure sensor at the outlet of the first evaporator; a first evaporator outlet isolation valve positioned in an outlet of the first evaporator, the first evaporator outlet isolation valve being arranged to prevent migration of refrigerant from the second evaporator outlet to the first evaporator outlet; wherein the first evaporator outlet isolation valve is an electronically controlled valve; characterised in that the controller monitors a superheat at the first evaporator based on the temperature and/or pressure at the evaporator outlets and generates a control signal to close the first evaporator outlet isolation valve in response to the superheat at the first evaporator. a compressor having a suction port and a discharge port, the compressor suction port coupled to a compressor inlet path; a heat rejecting heat exchanger downstream of the compressor discharge port; a first evaporator expansion device downstream of the heat rejecting heat exchanger; a first evaporator having an first evaporator inlet coupled to the first evaporator expansion device and a first evaporator outlet coupled to the compressor inlet path, the first evaporator for cooling a first compartment of a container; a second evaporator expansion device downstream of the heat rejecting heat exchanger; a second evaporator having a second evaporator inlet coupled to the second evaporator expansion device and a second evaporator outlet coupled to the compressor inlet path, the second evaporator for cooling a second compartment of the container; a controller; a first evaporator outlet temperature sensor and first evaporator outlet pressure sensor at the outlet of the first evaporator; a first evaporator outlet isolation valve positioned in an outlet of the first evaporator, the first evaporator outlet isolation valve being arranged to prevent migration of refrigerant from the second evaporator outlet to the first evaporator outlet; wherein the first evaporator outlet isolation valve is an electronically controlled valve; characterised in that the controller monitors a superheat at the first evaporator based on the temperature and/or pressure at the evaporator outlets and generates a control signal to close the first evaporator outlet isolation valve in response to the superheat at the first evaporator.