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ABSTRACTHistorically, research involving Indigenous peoples has been the scene of power imbalances between Indigenous communities and researchers. Indigenous peoples have often been put in the position of passive subjects of research rather than participants or collaborators with agency, a situation that the current movement of decolonisation of research and practices in the field of Indigenous health aims to counteract. Participatory research seeks a better balance of input, decision-making and power between research participants and research teams and values participants’ knowledges. As such, it is a particularly relevant approach for researchers to involve community members and support self-determination of Indigenous people. Yet, if its explicit intentions are aiming at a decolonising approach, the socio-structural context of participatory research initiatives in Indigenous communities brings obstacles to the approach’s success. The development and implementation of the participatory project Atautsikut: A Community of Practice in Youth Mental Health and Wellness in Nunavik, has been an occasion to document certain barriers that take place in participatory research. This article describes Atautsikutas a starting point for a reflection on the challenges of decolonising participatory research. It discusses how, despite intentions, structural barriers, blind spots and unexpected contextual elements may challenge the journey towards decolonising research.