A method and a framework for the application of Simulation-based Multi-objective Optimisation (SMO) has been developed in order to enhance the prerequisites for decision-making within design and re-configuration of production systems. This kind of decisions often tends to be based on financial information rather than the type of production system parameters to be found in traditional simulation models. Therefore, to combine traditional parameters with new financial and sustainability parameters can be very beneficial for supporting industrial decision-making. The framework has been applied in a number of case studies involving a range of production system issues both within component production and assembly operations. Several types of issues have been explored involving analysis of system behaviour, optimisation of sustainability parameters, in the form of energy consumption aggregated to energy cost, and optimisation of financial parameters in combination with traditional production system metrics. The case studies have adequately proven and verified that the application of SMO, especially including financial functions and objectives, can be very valuable for practical industrial applications.