This paper focuses on a production planning problem in a highly automated manufacturing system considering multiple process plans with different energy requirements. The system consists of several closely interconnected sub-systems such as the processing system, the material (part) handling system, the tool transport system and the auxiliary system responsible for a supply of cooling/lubricants and a waste disposal. We propose a methodology for an estimation of energy consumption and material flows that are incurred at a system level with respect to multiple process plans for a part type. In addition, this study focuses on a production planning problem with the objective to minimize the weighted sum of energy consumption, inventory holding cost and backorder cost on a FMS considering multiple process plans. The production planning model is developed as a linear programming model. The benefit coming from the adoption of suggested model has been addressed with reference to a real industrial use case study.