BACKGROUND: Healthcare associated infections (HAIs) are the most frequent adverse outcome in healthcare delivery worldwide. In conflict-affected settings HAIs, in particular surgical site infections, are prevalent. Effective infection prevention and control (IPC) is crucial to ending avoidable HAIs and an integral part of safe, effective, high quality health service delivery. However, armed conflict and widespread violence can negatively affect the quality of health care through workforce shortages, supply chain disruptions and attacks on health facilities and staff. To improve IPC in these settings it is necessary to understand the specific barriers and facilitators experienced locally. METHODS: In January and February of 2020, we conducted semi-structured interviews with hospital staff working for the International Committee of the Red Cross across eight conflict-affected countries (Central African Republic, South Sudan, Democratic Republic of the Congo, Mali, Nigeria, Lebanon, Yemen and Afghanistan). We explored barriers and facilitators to IPC, as well as the direct impact of conflict on the hospital and its' IPC programme. Data was analysed thematically. RESULTS: We found that inadequate hospital infrastructure, resource and workforce shortages, education of staff, inadequate in-service IPC training and supervision and large visitor numbers are barriers to IPC in hospitals in this study, similar to barriers seen in other resource-limited settings. High patient numbers, supply chain disruptions, high infection rates and attacks on healthcare infrastructures, all as a direct result of conflict, exacerbated existing challenges and imposed an additional burden on hospitals and their IPC programmes. We also found examples of local strategies for improving IPC in the face of limited resources, including departmental IPC champions and illustrated guidelines for in-service training. CONCLUSIONS: Hospitals included in this study demonstrated how they overcame certain challenges in the face of limited resources and funding. These strategies present opportunities for learning and knowledge exchange across contexts, particularly in the face of the current global coronavirus pandemic. The findings are increasingly relevant today as they provide evidence of the fragility of IPC programmes in these settings. More research is required on tailoring IPC programmes so that they can be feasible and sustainable in unstable settings.