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Agroecology results from interactions at the boundaries of sciences, practices and politics in France and Brazil. Taking a discursive approach, we analyze the way in which two public agricultural research institutions, Embrapa (Empresa Brasileira de Pesquisa Agropecuária) and Inra (Institut national de la recherche agronomique) delineate these boundaries in the course of their agroecology agenda-setting. We show that their programming exercises are more or less dependent on national political contexts. This generates differing dynamics and framings of the notion of agroecology. Ahead of Inra, Embrapa, encouraged by the Lula government and rural social movements, integrated agroecology to legitimize an alternative research agenda dedicated to family farmers. This agenda suffers from the constraints of a divided and increasingly stormy agricultural and political context. Within Inra, agroecology helps (re)legitimize agronomy to respond to societal challenges, while rejecting the political radicalism of social movements. Since 2012 this research agenda has found an echo in the implementation of French agroecological public policy. Moreover, an analysis of internal debates in Inra reveals different framings of agroecology and some tensions regarding the boundary nature of agroecology. The debates revolve around the scientificity of agroecology and its capacity to become, or not, a ferment for social justice. Through this approach we shed light on the way agroecology is unsettling Inra’s strategy and that of Embrapa.