The current trend in universities is marked by integrating information technologies into their service delivery. Particularly in administration and management, processes are being modernized, although not successful in some institutions. This study aims first to understand the complexity of an integrated educational management information system (UR-IEMIS) at the University of Rwanda and then to evaluate the degree of its diffusion in university services. Complex Adaptive System and Innovation Diffusion theories were used as a conceptual framework for this study. Document survey, observations, and interviews were used for data collection. Findings indicate that the UR-IEMIS is characterized by the complexity features as it is composed of several different subsystems (Organism, Roles, Objects, Method, and Concept) which emerge, interact, co-evolve, and re-organize to adapt to the disruptive institutional structures. It was also revealed that the UR-IEMIS integration is still at the abstraction level for all subsystems while for only few university functions, the system is diffused at knowledge, persuasion, and decision stages. Likewise, concerns related to the current unsatisfactory state of UR-IEMIS integration and proposals for improvement are discussed. Further studies should explore the complexity and diffusion levels for E-learning systems that support pedagogical activities in a similar case study context.