A collective project was developed to build research agendas for academic programs; as a prospective strategy to prioritize areas of action, use of resources and institutional capacities in a relationship between the university and the productive sectors of the region, from the development of intervention and study strategies, in 11 training scenarios. A collaborative and interdisciplinary methodology in the analysis of documents related to development, science and technology, allowed identifying common productive sectors of interinstitutional interest for the development of engineering programs of Systems and Industrial Engineering, analyzing their performance, good practices in research, technological surveillance of research centers, prioritize emerging thematic areas, build research intervention strategies and generate project profiles. The strategy gives greater relevance to the training of professionals, establishes a path of knowledge construction in areas of interest; that immersed in the curriculum plan; allow articulating research units in framework projects by research lines. The article presents significant aspects of the methodological route in the construction of these agendas, focused on two academic programs of the faculty of engineering.