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Healthcare-associated infections (HAIs) constitute a major contributor to morbidity and mortality worldwide, with a greater burden on low- and middle-income countries. War-related injuries generally lead to large tissue defects, with a high risk of infection. The aim of this study was to explore how physicians in a middle-income country in an emergency setting perceive HAI and antibiotic resistance (ABR). Ten physicians at a Jordanian hospital supported by Médecins Sans Frontières were interviewed face-to-face. The recorded interviews were transcribed verbatim and analyzed by qualitative content analysis with an inductive and deductive approach. The participants acknowledged risk factors of HAI and ABR development, such as patient behavior, high numbers of injured patients, limited space, and non-compliance with hygiene protocols, but did not express a sense of urgency or any course of action. Overuse and misuse of antibiotics were reported as main contributors to ABR development, but participants expressed no direct interrelationship between ABR and HAI. We conclude that due to high patient load and limited resources, physicians do not see HAI as a problem they can prioritize. The knowledge gained by this study could provide insights for the allocation of resources and development of hygiene and wound treatment protocols in resource-limited settings.