As the world grappled with the COVID-19 pandemic, healthcare workers (HCWs) continued to provide uninterrupted health care service delivery; therefore, this disproportionately affected their wellbeing. Our study explored the wellbeing of HCWs during the COVID-19 era in public health facilities in the City of Johannesburg, Gauteng province, South Africa. A qualitative study was conducted among twenty (20) HCWs through face-to-face in-depth interviews (IDIs) in the form of semi-structured interviews, audiotapes, and transcribed verbatim, and thematically analyzed with NVivo version 10. The findings showed that over half of HCWs (aged between 27 and 60 years) tested positive for COVID-19. Also, one third of HCWs' family members tested positive while some died due to COVID-19 infection. Informed by the workers' wellbeing framework, four themes emerged with fourteen sub-themes. Firstly, unsafe work environment was characterized by human resource related challenges such as increased workload; staff shortage; insufficient resources, e.g., personal protective equipment (PPE); poor policies in terms of compensation/allowance for being infected with COVID-19; poor health services; and death of colleagues. Secondly, poor health outcomes were described as strained emotional (psychosocial distress) and physical (respiratory related conditions) wellbeing. Thirdly, home and community environments were negatively impacted by interrupted relationships with family and friends, and experiences of deaths of loved ones. Finally, HCWs engaged personal wellbeing strategies through self-motivation; staying positive; family support; and participating in resilience-promoting extra mural activities to cope during the pandemic. In conclusion, the wellbeing of HCWs was aggravated during the COVID-19 era and led to low morale and compromised healthcare quality. This study advocates for promotion of greater resilience, and psychological and physical safety of HCWs through evidence-based, multilevel-multicomponent interventions at the workplace, home, and community environments in addition to strengthening public health policies and response to future pandemics.