BACKGROUND: Retention of skilled midwives is crucial to reducing maternal mortality in rural areas; hence, Cambodia has been trying to retain at least one secondary midwife who can provide basic emergency obstetric care at every health centre even in rural areas. The factors influencing the retention of midwives, but not solely secondary midwives, have been identified; however, the security issues that affected female health workers during the conflict and the post-conflict years and gender issues have been unexplored. This study explores these and other potential factors influencing secondary midwife retention and their significance. METHODS: Sequential two-stage qualitative interviews explored influential factors and their significance. The first stage comprised semi-structured interviews with 19 key informants concerned with secondary midwife retention and in-depth interviews with eight women who had deliveries at rural health centres. Based on these interview results, in-depth interviews with six secondary midwives who were deployed to a rural health centre were conducted in the second stage. These midwives ranked the factors using a participatory rural appraisal tool. These interviews were coded with the framework approach. RESULTS: Living with one's parents or husband, accommodation and security issues were identified as more significant influential factors for secondary midwife retention than current salary and the physical condition of the health centre. Gender norms were entrenched in these highly influential factors. The deployed secondary midwives who were living apart from one's parents or spouse requested transfer (end of retention) to health centres closer to home, as other midwives had done. They feared gender-based violence, although violence against them and the women around them was not reported. The health workers surrounding the midwives endorsed the gender norms and the midwives' responses. The ranking of factors showed similarities to the interview results. CONCLUSIONS: This study suggests that gender norms increased the significance of issues with deployments to rural areas and security issues as negative factors on female health workforce retention in rural areas in Cambodia. This finding implies that further incorporating gendered perspectives into research and developing and implementing gender-responsive policies are necessary to retain the female health workforce, thereby achieving SDGs 3 and 5.