Smart cities have frontline responsibility to ensure a secure and safe physical and digital ecosystem promoting cohesive and sustainable urban development for the well-being of EU citizens. S4AllCities integrates advanced technological and organizational solutions in a market-oriented unified Cyber–Physical Security Management framework, aiming at raising the resilience of cities’ infrastructures, services, ICT systems, IoT and fostering intelligence and information sharing among city’s security stakeholders. Three pilot cases, with the engagement of a total of 5 cities in 4 countries (Spain, Romania, Czech Republic, Greece), enable S4ALLCITIES System of Systems to deploy and validate its intelligent components and functionalities in an actual environment, ensuring the delivery of solutions and services in line with smart cities emerging requirements, focused on: risk-based open smart spaces security management; cyber security shielding; suspicious activity and behavior tracking; identification of unattended objects; real-time estimation of cyber-physical risks in multiple locations and measures activation for effective crisis management.