A multi-compartment transport refrigeration system (10) includes a first evaporator (40) having an first evaporator inlet coupled to a first evaporator expansion device (140) and a first evaporator outlet coupled to a compressor inlet path, the first evaporator for cooling a first compartment of a container at a first temperature; a second evaporator (609 having a second evaporator inlet coupled to a second evaporator expansion device (160) and a second evaporator outlet coupled to the compressor inlet path, the second evaporator for cooling a second compartment of the container at a second temperature greater than the first temperature; and a controller (550) for controlling the first evaporator expansion device in response to a first superheat setpoint and controlling the second evaporator expansion device in response to a second superheat setpoint, the controller adjusting the second superheat setpoint in response to the second temperature and the first temperature.