A multi-compartment transport refrigeration system comprising: a compressor having a suction port, a discharge port and an intermediate inlet port located at an intermediate location along a compression path between the compressor suction port and the compressor discharge port; a heat rejecting heat exchanger downstream of the compressor discharge port; an economizer heat exchanger having a first refrigerant flow path and a second refrigerant flow path therethrough; a first evaporator expansion device downstream of the first refrigerant flow path; a first evaporator having an inlet coupled to the first evaporator expansion device and an outlet coupled to a compressor inlet path, the compressor inlet path coupled to the compressor suction port, the first evaporator for cooling a first compartment of a container; a second evaporator expansion device downstream of the first refrigerant flow path; a second evaporator having an inlet coupled to the second evaporator expansion device and an outlet coupled to the compressor inlet path, the second evaporator for cooling a second compartment of the container; an economizer expansion device coupled to the first refrigerant flow path, the economizer expansion device directing refrigerant from the first refrigerant flow path to the second refrigerant flow path, the second refrigerant flow path coupled to the intermediate inlet port; an engine to provide power to the compressor; a controller controlling the economizer expansion device to regulate flow of refrigerant along the second refrigerant flow path to the intermediate inlet port characterised in that the controller controls the economizer expansion device in response to operating parameters of the engine. a compressor having a suction port, a discharge port and an intermediate inlet port located at an intermediate location along a compression path between the compressor suction port and the compressor discharge port; a heat rejecting heat exchanger downstream of the compressor discharge port; an economizer heat exchanger having a first refrigerant flow path and a second refrigerant flow path therethrough; a first evaporator expansion device downstream of the first refrigerant flow path; a first evaporator having an inlet coupled to the first evaporator expansion device and an outlet coupled to a compressor inlet path, the compressor inlet path coupled to the compressor suction port, the first evaporator for cooling a first compartment of a container; a second evaporator expansion device downstream of the first refrigerant flow path; a second evaporator having an inlet coupled to the second evaporator expansion device and an outlet coupled to the compressor inlet path, the second evaporator for cooling a second compartment of the container; an economizer expansion device coupled to the first refrigerant flow path, the economizer expansion device directing refrigerant from the first refrigerant flow path to the second refrigerant flow path, the second refrigerant flow path coupled to the intermediate inlet port; an engine to provide power to the compressor; a controller controlling the economizer expansion device to regulate flow of refrigerant along the second refrigerant flow path to the intermediate inlet port characterised in that the controller controls the economizer expansion device in response to operating parameters of the engine.