The role of humanitarian organizations is becoming increasingly vital in a world characterized by conflicts, natural and man made disasters, and disease epidemics. For these organizations to be-come more effective, they need robust supporting information systems. These systems are complex to design and use for two reasons. One, the context is unstable, unpredictable and extremely dynamic. Two, the methods for design of these systems typically follow structured methods assuming routine information systems. There is thus a mismatch resulting in emerging contradictions, which in the short-run have adverse consequences, but in the longer run provide the potential for positive change. Theoretically, we draw upon some concepts from institutional theory, such as institutions, logics and contradictions to understand what are the emerging contradictions, why do they occur, and what can we do about them. Empirically, we study a large humanitarian organization (MSF), and analyze some of their processes around the design and development of their “humanitarian health management information system.” We identify contradictions arising from various technical, institutional and contextual conditions, and analyze how the potential for change carried in them can be positively leveraged upon.