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Abstract Background According to the Internal Displacement Monitoring Centre report on global human displacement, Ethiopia has the highest number of newly displaced people forced to flee their homes. Displaced people have arrived in other regions, sometimes leading to conflict. Several regions in Ethiopia experience on-going ethnic tensions and violence between tribes, which leaves smallholder farmers suspicious of any outside activities in their locale, assuming other ethnic groups may harm them. Changes in the central Ethiopian government have also led to suspicion of non-local agencies. The Campylobacter Genomics and Enteric Dysfunction (CAGED) research project’s objective is to improve the incomes, livelihoods and nutrition of smallholder farmers and was conducted during this period of increasing violence. The project aims to assess the impact of reducing exposure to chicken excreta on young children’s gut health and growth. This paper does not report empirical findings from CAGED, but is part of a series that aims to identify challenges in humanitarian research and reports on mitigation strategies during this research. Discussion This research is important to determine whether Campylobacter infection in chicken’s contributes to illness and stunting in children. However, violence against other researchers in different parts of Ethiopia led to mistrust and lack of engagement by the community with the researchers. Some reactions were so hostile that the team was fearful about returning to some households. As a result, the team designed strategies to respond, including establishing two types of community advisory boards. One used pre-existing village elder structures and another was composed of village youth. Data collection team members received training in principles of ethics, consent, and crisis management, and were provided on-going support from local and international principal investigators and the study’s ethics advisor. Conclusion The hostility and mistrust led to fear among the data collectors. These and the resulting strategies to address them resulted in delays for the research. However, the interventions taken resulted in successful completion of the field activities. Moreover, the lessons learned from this project are already being implemented with other projects being conducted in various parts of Ethiopia.