Researchers and practitioners present entreprise integration to a Supply Chain as a lever for organizational performance. Yet if integration is generating performance, this cannot be done without the acceptance of new constraints due to integrated information systems implementation. We discuss the evaluation of the information systems that support the integration in order to uncover some negative consequences associated with their use. We mobilize the concept of undesirable effects and thus pose our research question: How can we identify and assess undesirable effects for users of integrated information systems or interorganizational systems? We analyze the perceptions of users on the effects of regular use of technology for their logistics activity. We adopt a qualitative methodology and select two case studies of just-in-time supply chain in the food and automotive industry. Data collection is carried out through interviews and analyzed by thematic coding. The results lead to identify twelve undesirable effects, four of which are specific to the use of interorganizational information systems. These results may extend the typology of misfits of Strong and Volkoff (2010) by entering the notion of undesirable effects to assess the negative consequences for users of the use of integrated information system.