Urban railway transit systems in big cities operate at high capacity and represent the main arteries of city transport networks. In current operations, infrastructure failures occur occasionally causing severe disruptions. In this research, we propose a novel integrated disruption management methodology for automatically rescheduling trains and controlling passenger flows for a given disruption. Our framework incorporates a train traffic management model together with a model for adjusting flows of passengers and aims to minimize the total delay of passengers, the number of denied passengers, adjustments to train services, and recover time. On the train side, we short-turn, cancel and reroute train services. On the passenger side, we reflow passengers according to a disrupted timetable and control station gates. We test our integrated disruption management approach on real-life cases and discover dependencies between delayed/denied passengers and traffic management. Our goal is developing practical solutions to this critical transportation problem that will lead to establishing advanced decision support systems to assist metro dispatchers.