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The authors start by acknowledging that, in response to the specificities of research on issues to the environment, sustainable development and the socio-ecological transition (taking into account their complexity and action-orientation), two successive innovations have emerged: interdisciplinarity and participatory research. The authors refer to the notion of ‘research regime’ to question what has happened with the first – which reached its peak in the 80’s – in order to draw lessons for the second, which is on the rise since the 2000’s. They consider that interdisciplinarity has not succeeded in becoming an acknowledged research regime, due to lacking further in depth investigation of its practical and epistemological foundations. They conclude that, despite its increasing attraction, participatory research runs the same risk if it also omits investigating deeper into its foundations. They outline orientations for the research policy needed to overcome this risk. At stake is the establishment of a research regime particularly adapted to addressing the concerns and demands of the social and ecological transition.