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As the prevalence of conflict and fragility continue to rise around the world, research is increasingly heralded as a solution. However, current ethical guidelines for working in areas suffering from institutional and social fragility, insecurity or violent conflict have been heavily critiqued as highly abstract; focussed only on data collection; detached from the realities of academia in the Global South; and potentially extractive. This article seeks to respond to that assessment by spotlighting some of the most prevalent challenges researchers face in the pursuit of ethical working practices. It explores the material and epistemic injustices that often shape and underpin research structures and relationships in these contexts. The paper draws on the authors’ experiences of research in conflict-affected and fragile contexts over the last fifteen years and on workshop discussions with researchers based in fragile and conflict-affected contexts conducted in Amman, Bogotá and Dhaka in 2019-2020. The paper works from the premise that achieving ethical research in fragile spaces is not dependent solely on activity at the site of research, but also on decisions made across the entire ecosystem of a research project. It therefore interrogates the full research landscape, from funding models, to research design, to dissemination plans and ethical gatekeeping. The paper critically reflects on inequities in the processes of knowledge production about conflict and fragility and the key ethical challenges that researchers encounter. It highlights the need for further guidance, support and accountability to ensure ethical research practices.