This paper analyzes the interoperability issues of the information exchange among essential software applications that enable University electronic services. The analysis of the existing standards shows that there is no fully defined compatibility for these software solutions, which motivated us to conduct a research in order to detect and describe the interoperability challenges of creating a fully automated interaction. In this paper we present several case studies of challenges faced at our University, while integrating three existing different systems: iKnow as a custom developed university management system, a customized version of an open source Moodle learning management system and e-Testing as a custom developed e-assessment system. Although these systems operate independently, still there are many interactions among them; keeping the system consistent and tightly connected at the same time. Keeping the software development compliant with the elaborated standards and enabling a push or scheduled synchronization modules will eliminate a big maintenance effort to enabling interoperability with new software versions or when migrating to another type of service provider.