Decision making in new technologies is a crucial activity to raise competitiveness, especially for technology organizations. The decision-making process requires the use of information technology tools, since the information amount is large and requires reliable methods for collecting, accessing, storing, processing, distributing, and evaluating, in order to provide reliable information to decision makers. The strategy of an organization must take into account the integration of this aspect with other organizational functions. This paper presents a proposal to integrate new elements into the IT strategy, considering the interactions with other organizational functions, defining an implementation and transition plan that takes into account the organization dynamics, which has limited resources and, therefore, requires a gradual and long term transition plan. This paper refers as case study to a Mexican Public R&D Center, which has re-engineered its operating model with a systems approach.