The article reflects on the contradictions characterizing the processes of knowledge production in the context presented by demands from social movements and other actors resulting from socio-environmental crises and conflicts. Through a consideration of the experiences of the scientific sector in Brazil since the 1980s, the work explores the development of initiatives oriented at supporting the social struggles against diverse forms of socio-environmental injustice and inequality, emphasising the obstacles facing the attempts to produce knowledge that transcends disciplinary frontiers. These obstacles include the intrinsic difficulties characterizing the production of scientific knowledge and the impediments derived from the hegemonic forms of disciplinary purism and the institutional organization of the scientific system. The article discusses encouraging examples of interdisciplinary practices committed to the defence of human rights and environmental justice, and highlights the confrontations oriented at transcending disciplinary barriers as an essential aspect of the development of scientific knowledge.