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Employees were required to adopt new working methods within a very short time frame during the COVID-19 period through digitalization. While digitalization has been largely perceived as an enabler during the pandemic, its impact on employee health and well-being remains complex and underexplored, particularly in the public sector, where employees have less discretion to adapt digital tools. This study examines how rapid workplace digitalization during COVID-19 affected employee health and well-being in the public sector. Drawing on the job demands–resources (JD-R) framework, we focus on three specific forms of digital work—digital meetings, digital clearance, and digital training—selected because they represent distinct theoretical pathways through which digitalization affects well-being, such as digital meetings and digital training can increase job demands that can deplete employee energy and increase stress, whereas digital clearance operates as a job resource that reduces bureaucratic hurdles and enhances autonomy. To test these ideas, this study uses data from the 2020 Australian Public Service Commission Census (n = 108,085), and applies ordinal and multinomial generalized structural equation modeling (GSEM) to assess the effects of three new ways of working—digital meetings, digital clearance, and digital training—on employees’ health and well-being, as well as the mediating roles of organizational support. The results demonstrate that while digital clearance is positively associated with employee health and well-being, digital meetings and digital training are negatively associated. Organizational support mediates these relationships, underscoring its importance in mitigating adverse effects. These findings highlight the mixed consequences of digitalization for public employees’ health and well-being and point to the need for supportive organizational strategies in times of crisis. As a practical implication, this study suggests that public sector organizations should prioritize employee mental health in teleworking policies, adopt employee-centered digital transformation strategies that provide adequate resources and training support, and implement digital clearance processes that enhance employee well-being, particularly during a crisis.