The paper concerns the analysis of the impact of organizational changes in the Research Institute on its activities in the field of commercialization of innovations. Tools such as SWOT analysis and process mapping were used for the analysis. The paper shows how a change in the organizational structure can optimize the operation of the Research Unit. This paper describes an organizational change in the structure of the department responsible for conducting research and development projects and commercializing their results. This change resulted from a complete reorganization of the unit under study (strategic integration of three research and development units with different scopes of activity, but the same area of activity). The main part of this paper concerns the restructuring of the previously independent research institute, which received the status of a technology center, within a new, integrated organizational structure. This resulted, on the one hand, in a shift in the scope of some auxiliary activities and a change in decision-making paths within the new organizational structure. Hence, the old organizational structure became much less effective on the market. Therefore, both the previous and the changed organizational scheme were presented in the paper. The change in decision-making paths resulting from the introduced organizational changes was also presented. The effect of the introduced organizational changes is the adaptation of the technology center’s activities to the commercialization strategy adopted in the new organization. By eliminating duplicate organizational units and decision-making processes, the synergy of activities has increased. In addition, the merger of departments has shortened the time of introducing newly developed solutions to the market.