The machine loading (ML) problem of flexible manufacturing systems (FMS) has been recognized as one of the most important planning problems in industry. This study aims to minimize the system unbalance developing a modified binary bat algorithm (MBBA), satisfying the technological constraints such as the availability of machine time and tool slots. The proposed algorithm was implemented in Matlab ® , and to show its application, a case study was conducted on a major Italian company, which manufactures equipment and plants for the food industry. Two scenarios are evaluated to this end: an “AS IS” scenario, reflecting the current configuration of the production system, and a “TO BE” one, in which the MMBA is implemented for improving the system’s performance. For the TO BE scenario, a new sequence of jobs, able to minimise the variance of the total processing time, was determined. The application of the MMBA reveals significant improvements in processing time compared to the current approach used by the company. The results of the TO BE scenario can be used to provide effective indications to operations managers, helping them to identify an alternative strategy to enhance the efficiency of the targeted production system.