In this work, the possibility of limiting energy consumption in the manufacturing process of bioethanol to obtain biofuel was analysed. For this purpose, a control algorithm has been optimised while retaining the good quality of the control signals. New in this study is the correlation of the control algorithm not only with the signal’s quality, but also with the energy consumption in such an energy-intensive process as rectification. The rectification process in a periodic production system has been researched. The process was modelled on a test station with the distillation mixture capacity of 25 dm3. For the optimization, the following control algorithms have been applied: relay, PID and PID after modification to I-PD. The simulation was carried out on a transfer function model of the plant that has been verified on a real object, a rectification column. The simulations of energy consumption and control signal’s quality have been carried out in the Matlab®-Simulink environment after implementing the model of the research subject and control algorithms. In the simulation process, an interference signal with an amplitude of 3% and frequency of 2 mHz was used. The executed analyses of the control signal quality and the influence of the control algorithm on the energy consumption has shown some essential mutual relationships. The lowest energy consumption in the rectification process can be achieved using the I-PD controller—however, the signal quality deteriorates. The energy savings are slightly lower while using the PID controller, but the control signal quality improves significantly. From a practical point of view, in the considered problem the best control solution is the classic PID controller—the obtained energy effect was only slightly lower while retaining the good quality of the control signals.