This paper discusses the development of the Aerospace Performance Factor (APF) methodology in a real case implementation. The research presents to ATM safety managers and researchers the main framework and the roadmap to develop a specific system-wide assessment, giving them guidelines based on lessons learned. Starting from international regulations and describing the European APF context, this paper offers a detailed description of the APF implementation to the Italian Air Navigation Service Provider ENAV s.p.a., one of the first ANSPs to adopt, customize and implement the methodology.