A control system for controlling a machine (1) for the temperature processing of containers (3) for food products, having a movement element (2) for moving containers (3) to be processed on a movement path along which at least one temperature-processing zone (6) is defined, in particular where the temperature of the containers (3) is lowered, the temperature-processing zone being divided into sub-zones (6a-6c) each having a respective injection assembly (8) for injecting processing fluid (9) on the containers (3) and a respective adjusting assembly (17, 18, 19) for setting the temperature of the injected processing fluid. The control system is provided with a control unit (20) coupled to the adjusting assemblies of the sub-zones (6a-6c) for regulating the temperature of the processing fluid, by performing a prediction of the output temperature of the containers located on the movement path, i.e. a temperature the containers would reach at output from the temperature-processing zone, based on a current operating condition of the machine (1) and a past thermal trend for the containers and controlling the adjusting assemblies based on the predicted output temperature.
