The article discusses the specificities of science and technology development and innovation processes in organizational arena and their implications for planning and management. It proposes that ST&I processes must be planned and managed as evolutionary processes defined by targeted attitudes to search routines and an understanding of the selective instances in which organizations are embedded, taking into consideration the distinct institutional elements that mediate such relations. To deal with this framework, the article proposes a methodological framework comprising a set of building blocks to help managers deal with the challenge of innovation. The building blocks are: (1) indeterminacy; (2) the profile of the professionals involved and the organizational culture; (3) the collective logic associated with the complexity of non-linear, dynamic and adaptive systems; and (4) the logic of the scope economies associated with knowledge production. The methodology is applied in a case study of the Brazilian Agricultural Research Corporation, Embrapa.