This paper addresses methodological issues of conducting research with communities that have been subjected to colonial rule in different forms and, as a result, have been excluded from knowledge production processes. In particular, I explore the ways in which the Kurdish and Zapatista movements have pursued a project of decolonizing knowledge by engaging in critique of modern Western science and by developing alternative approaches to knowledge production. The two movements can help us challenge the basic assumptions about what constitutes the legitimate spaces for knowledge production and who are the legitimate agents of this process: Do we as academics take seriously analytical categories and theories developed by movements and communities in struggle? Does the knowledge produced by these actors stand on equal footing with the knowledge produced by academia? What agency should those who are researched upon have in setting the terms of research and formulating its conclusions? Whom and what goals does research serve? I argue that the intellectual contributions developed by these two movements provide us with some ways forward towards decolonizing and transforming conventional methodological approaches and epistemological underpinnings of academic research. I explore in particular how the two movements have challenged three features of mainstream research in social sciences – Western-centrism, positivism and academia-centrism – which have enabled persisting exclusion and marginalization of oppressed communities in struggle within the institutions of knowledge production. In addition, I discuss three features of alternative knowledge production which can be identified from the two movements’ discourse and practice, namely transcending separation between theory and practice; producing situated knowledge; and collectivizing and democratizing knowledge production. In the process, I make a case that social movements do produce knowledge; yet, this knowledge differs from the one produced purely within academia in that there is no separation between theory and practice. As such the type of knowledge produced and advocated by the Kurdish and Zapatista movements echoes what Boaventura de Sousa Santos calls “epistemologies of South,” that is, knowledge produced through involvement in a social and political struggle. Finally, in seeking ways forward for social science research, the paper explores the potential of collaborative or participatory research for “decolonizing” the relationship between researchers and their interlocutors and engaging with the movements as legitimate knowledge producers. I draw primarily on texts, speeches, and interviews by the members and representatives of the two movements which address questions of knowledge production.