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Increasing evidence of the effects of the COVID-19 pandemic on healthcare workers’ mental health and wellbeing has prompted concerns about the longer-term impacts on healthcare delivery and health workforce sustainability. For rural health services and communities, the pandemic has compounded existing challenges including workforce shortages, potentially leading to further health inequalities. This qualitative interview study aimed to explore factors within and external to the health service environment that influenced health service staff mental health and wellbeing in rural and regional Victoria, Australia, during the first two years of the COVID-19 pandemic (2020-2021). Participants were recruited from nine publicly funded rural and regional health services. Semistructured interviews were conducted via videoconference, audio-recorded, and transcribed. Data were analysed using a five-stage framework approach. Eighteen health service staff from four rural areas participated in the study. A range of factors that were perceived by participants to influence their wellbeing were identified. These were coded to four main themes: (1) rural community relations, (2) the nature of the health workplace, (3) self-care and supportive networks, and (4) public health measures and the unpredictable nature of the pandemic. Factors coded to these themes were described as both positive and negative influences on health staff mental health and wellbeing. Optimising the mental health and wellbeing of rural health staff is imperative to the sustainability of this workforce during and beyond the COVID-19 pandemic. Rural health services must consider the community and health service (meso-level), individual (microlevel), and broader pandemic context (macrolevel) when developing and implementing strategies to promote staff wellbeing. Strategies must encompass the development of senior leadership capabilities, mechanisms to support effective leadership, and optimal communication processes within health services. Given the potential for community support to positively influence rural health staff wellbeing, community engagement should be a feature of health service wellbeing strategies.