Research programs referring to agroecology increased during the past decade. They seek to generate knowledge and innovations to support transition processes in agriculture, as related with food and environment. They also intend to develop alternative research methods (interdisciplinarity, partnership, participatory) and topics (sustainable food systems, ecosystem services)..A body of research is being developed among different groups and organizations by Embrapa in Brazil from 2006, and more recently by INRA in France. Based on a description of each situation and a comparative approach between both public and national research organizations, we analyze the institutionalization process of agroecology. Beyond public consultations and pressure from social movements, a renewal of research management, approaches and outcomes is also at stake. It is supported by national and international initiatives. We also discuss the practical conditions and opportunities for the advancement of knowledge and the contribution of agroecology in research and in the development of agricultures.