More often, the decisions of part selection, machine loading, machining optimisation and part scheduling sub-problems are made at different decision-making levels. As a result, part selection, machine loading and machining optimisation decisions at higher-production planning level may fail to interact with part scheduling decisions at lower-scheduling level. This paper presents a two-stage sequential methodology aimed at integrating the decisions of part selection, machine loading, machining optimisation and part scheduling sub-problems for flexible manufacturing systems (FMSs) and avoiding disparities of decisions which can be difficult to implement on the FMS shop floor. In this case, two mathematical models were presented and solved. Results from the models show that more interactive decisions and well-balanced workload of the FMS can be achieved when part selection, machine loading, machining optimisation and part scheduling sub-problems are solved jointly.