Background <p>Occupational well-being is a key element of employee health and a crucial determinant of productivity. The present exploratory study investigates longitudinal changes in work engagement and exhaustion as indicators of occupational well-being during different stages of the COVID-19 crisis among employees in Switzerland and Germany.</p> Methods <p>Using a four-wave panel design, we collected data from 2,137 participants during various stages of the pandemic from April 2020 to December 2021. We applied latent change score modeling to examine changes within groups and differences between employee groups over time.</p> Results <p>Results show that work engagement declined significantly between April and July 2020, partially recovered between July and December 2020, and then remained stable until December 2021. Multi-group analysis highlighted the importance of national context, social connections, and work flexibility as working in Switzerland, living with others, caregiving responsibilities for children, and remote work were consistently associated with higher work engagement. In contrast, exhaustion levels remained relatively stable across all time points. However, some significant differences emerged between groups, with employees in Switzerland reporting an overall lower level of exhaustion. Age-specific trends were also identified, with older employees reporting overall lower levels of exhaustion compared to younger employees across the whole measurement period.</p> Conclusion <p>The study contributes to the understanding of the dynamic nature of occupational well-being during the pandemic, with implications for organizations aiming to support their employees not only in times of crises.</p>