This book constitutes the refereed proceedings of the Second Conference on Security of Industrial Control Systems and Cyber-Physical Systems, CyberICPS 2016, held in Crete, Greece, in September 2016 in conjunction with ESORICS 2016, the 21st annual European Symposium on Research in Computer Security. The 5 revised full papers  2 invited papers presented were carefully reviewed and selected from 18 initial submissions. CyberICPS 2016 focuses on topics related to the management of cyber security in industrial control systems and cyber-physical systems, including security monitoring, trust management, security policies and measures.