A new era of higher education in Debrecen began in 2000 – decades after the 1912 founded state university was split into several institutions in 1950 – the Debrecen University was established from four independent institutions, offering the broadest range of study programs in the country with five university faculties, three college faculties, nine institutes and three associated institutions. This study reviews the preliminary steps which had been taken to prepare for the institutional integration within the framework of the Debrecen Universitas Association and the Debrecen University Association, describes the circumstances surrounded the failure of the direct integration of church institutions, and details the events connected to the launch of the new university, also presenting the recollections of those involved in the university leadership at the time. The success of the Debrecen University integration was based on its special characteristics, such as broad-based leadership, close cooperation of rectors elected for a short period from different fields of science, highly decentralized management, the establishment of the Medical and Health Sciences Center  and  the Agricultural Sciences Center – which combined high-level clinical work and agricultural activities, respectively, with the function of related faculties –, and an infrastructural investment program that enabled advances in the majority of educational areas and focused on support of scientific research. Based on the structural decisions, internal integration processes were launched for consolidated operation of informatics, the libraries and language departments, and in the activities of specialty coordination centers, to facilitate cooperation in educational programs and research work.  A constructive and harmonious relationship had been developed with the newly formed university-level students’ union and, within the framework of a collective agreement with the institution's employees. The cooperation agreement with the city of Debrecen, the interconnection with the Hungarian Academy of Sciences and participation in the founding of the European University Association were of decisive importance in the university's external relations. The joint works in developing the identity of the University of Debrecen, the creation of symbols and brand images linked to the historical Debrecen Reformed College resulted in trust-based cooperation and breaking down of barriers between the integrating communities of scholars, researchers, students, and employees.