Hospital Information Systems (HIS) are considering a significant aspect for supporting health care professionals in their work. However, a large number of them are often poor to provide the needed information for accomplishing various work activities in the oriented environment. The aim of this research is to address users’-Administrators and Clinicians- perceptions in order to gain a deeper knowledge about problems they encounter with daily work performed through IS. Additionally, the scope is extended into formulating suggestions through the employment of Soft System Methodology (SSM) that could bring improvements. A qualitative interpretive method with an inductive analysis was followed. Data collection completed through focus group interview sessions and the adoption of SSM three activities in order to acquire the complexity of the problem situation.   Research findings revealed that despite IS Lisora serves as a tool for supporting users work operations, it causes significant problems in their daily operations since the information flow are not feasible. Thus, the research study suggests five feasible and desirable improvements that could improve the overall processes followed by the hospital’s users and bring improvements. In all, SSM was proved to be very efficient in identifying problems that exist. In this way proposed solutions to the problems were enlightened. The general hospital of Preveza shall benefit from the higher efficiency offered by the system, which in turn shall improve the quality of health-care services offered.