This study develops a new optimisation framework for process inspection planning of a manufacturing system with multiple quality characteristics, in which the proposed framework is based on a mixed-integer mathematical programming (MILP) model. Due to the stochastic nature of production processes and since their production processes are sensitive to manufacturing variations; a proportion of products do not conform the design specifications. A common source of these variations is misadjustment of each operation that leads to a higher number of scraps. Therefore, uncertainty in misadjustment is taken into account in this study. A twofold decision is made on the subject that which quality characteristic needs what kind of inspection, and the time this inspection should be performed. To cope with the introduced uncertainty, two robust optimisation methods are developed based on Taguchi and Monte Carlo methods. Furthermore, a genetic algorithm is applied to the problem to obtain near-optimal solutions. To validate the proposed model and solution approach, several numerical experiments are done on a real industrial case. Finally, the conclusion is provided.