This paper analyzes the research performance evolution of a scientific institute, from its genesis through various stages of development. The main aim is to obtain, and visually represent, bibliometric evidence of the correlation of organizational changes on the development of its scientific performance; particularly, structural and leadership changes. The study involves six bibliometric indicators to multidimensionally assess the evolution of the institution’s performance profile. For a case study, we selected the Renewable Energy Institute at the National Autonomous University of Mexico, created 35 years ago as a small laboratory, then it evolved to a research center and finally to a formal institute, which over the last 8 years changed from the traditional departmental structure to a network-based structure. The evolution of the multidimensional performance profiles is analyzed, and graphically represented, using a novel artificial intelligence-based approach. We analyzed the performance profiles evolution yearly, using Principal Components Analysis, and a self-organizing neural network mapping technique. This approach, combining bibliometric and machine learning techniques, proved to be effective for the assessment of the institution’s evolution process. The results were represented with a series of graphs and maps that clearly reveal the magnitude and nature of the performance profile evolution, as well as its correlation with each of the structural and leadership transitions. These exploratory results have provided us data and insights into the probable effects of these transitions on academic performance, that have been useful to create a dynamical model.