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BackgroundPreventive care has gained increasing attention in health reforms around the world due to its ability to reduce the burden of disease and to save health costs. Nevertheless, there is a gap in terms of the development of reliable systems to measure and evaluate performance of preventive care in order to support decision-making and increase service outcomes. The aim of this study is to define a methodology for designing a performance management system (PMS) in order to effectively support the planning, control and evaluation of preventive care and to identify the factors that influence such a process.MethodsThe methodology is based on the participatory action research approach, which implies collaboration between researchers and practitioners. The study was articulated in four phases and carried out in an Italian regional healthcare system that was undergoing a major reorganization process.ResultsThe findings provide insights into the peculiarities that affect preventive care and highlight two categories of critical factors: general issues regarding the process and specific issues regarding preventive care. The first category includes the importance of interactions between academics, physicians and policy-makers, the impact of workloads and red tape on employee involvement and the increased conservation mechanisms during periods of institutional change. The second category concerns the strong heterogeneity of preventive activities within health organizations, the huge amount of regulations and the incompleteness of information systems.ConclusionThe development of a PMS for preventive care can best be served by collaborative methods that involve academics, professionals and policy-makers, whose roles and responsibilities must be clearly defined, and by an improvement in transparency and communication within organizations in order to enhance the involvement of different professionals at appropriate times and in appropriate ways. Key recommendations that may improve the maintenance and use of information systems are proposed to policy-makers.Electronic supplementary materialThe online version of this article (10.1186/s12913-018-3837-8) contains supplementary material, which is available to authorized users.