The rapid medical and technological progress and the resulting need for life-long learning lead to the proliferation of online-based programs in health informatics for health care and health informatics professionals. Effective learning in these online-based programs demands close interaction and cooperation between students and instructors. In such cooperative online-based programs, special emphasis is thus put on fostering a community of inquiry between all participants. The online-based master program on Health Information Management at the University UMIT is firmly based on the constructivist theory of situated learning in such a community of inquiry. Online activities in this master program are designed to promote social presence, cognitive presence and teacher presence as preconditions for successful learning. To verify whether these three forms of presences are visible and whether learning was successful, the first four six-week online-based modules with overall 60 participants were analyzed in depth, combining data from community of inquiry surveys, student evaluations, workload assessments and final assessment results. Results indicate that it was possible to build a community of inquiry (with scores of 4.2 and higher) and to foster effective learning. We conclude with recommendations on how to build a community of inquiry in online-based cooperative learning and also discuss some constraints.