The dynamics of changes in the market and the constantly increasing competition force entrepreneurs to continuously seek ways to improve process flexibility. Production flexibility depends, among other things, on machine setup parameters. In the context of flexibility, setup time plays an important role. The most popular tool used to reduce setup time is SMED. However, companies implementing SMED in their decision-making process consider not only setup times but also their costs, as well as aspects related to quality and safety. Despite the existence of methods supporting decision-making processes, in some companies, decisions about selecting workstations for improvement are still made subjectively. This article proposes a new method for prioritizing production workstations in the implementation of SMED. The method suggests planning setup improvements based on the priority index, which considers not only the setup times of individual production workstations but also financial, quality, and safety issues, taking into account the weights of individual factors. The method was developed in collaboration with a Polish automotive company, but it can be applied in any manufacturing enterprise where decision-making process support is needed.