Background: Hospital clinical staff have reported poor psychosocial wellbeing during the COVID-19 pandemic. Little is known about community health service staff who undertake various roles including education, advocacy and clinical services, and work with a range of clients. Few studies have collected longitudinal data. The aim of this study was to assess the psychological wellbeing of community health service staff in Australia during the COVID-19 pandemic at two time points in 2021. Methods: A prospective cohort design with an anonymous cross-sectional online survey administered at two time points (March/April 2021; n = 681 and September/October 2021; n = 479). Staff (clinical and non-clinical roles) were recruited from eight community health services in Victoria, Australia. Psychological wellbeing was assessed using the Depression, Anxiety and Stress Scale (DASS-21) and resilience using the Brief Resilience Scale (BRS). General linear models were used to measure the effects of survey time point, professional role and geographic location on DASS-21 subscale scores, adjusting for selected sociodemographic and health characteristics. Results: There were no significant differences in respondent sociodemographic characteristics between the two surveys. Staff’s mental health declined as the pandemic continued. Adjusting for dependent children, professional role, general health status, geographic location, COVID-19 contact status and country of birth; depression, anxiety and stress scores were significantly higher for respondents in the second survey than the first (all p < 0.001). Professional role and geographic location were not statistically significantly associated with scores on any of the DASS-21 subscales. Higher levels of depression, anxiety and stress were reported among respondents who were younger, and had less resilience or poorer general health. Conclusions: The psychological wellbeing of community health staff was significantly worse at the time of the second survey than the first. The findings indicate that the COVID-19 pandemic has had an ongoing and cumulative negative impact on staff wellbeing. Staff would benefit from continued wellbeing support.