This paper focuses on the process of implementing strategic information systems (SIS) by studying the radical changes it may bring to an organization’s deep structure. It argues that a full understanding of the process of implementation of such systems should include not only technical aspects but also the social dynamics of an organization; specifically core values, distribution of power and mechanisms of control. A theoretical framework is formulated based on punctuated equilibrium and previous SIS literature, and is applied to an exploratory case study conducted in a Latin American public organization. The case study depicts how the initiative to implement SIS was the result of external and internal disturbances. The case analysis highlights relationships between an organization’s deep structure and SIS implementation. The paper concludes by discussing the theoretical and practical implications of the study. These include (a) the role of the formal organizational structure in influencing the outcome of SIS implementations, (b) the impact of exogenous contingencies such as elections and external funding that may create a sense of crisis and (c) the influence of newcomers who may be brought in to solve the crisis.