The 2020 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic introduced unprecedented disruptions in both working conditions and social life. This lead to a variety of additional stressors for academics. The objective of this study was to determine the effect of the SARS-CoV-2 measures on academics, introduced during the first SARS-CoV-2 wave in Belgium, and to verify possible intervening variables in coping with these measures (stress management). The position, family and home situation of the respondents was checked. A cross-sectional study design was used. The study included 1837 respondents from the different Belgian universities. The overall mental and physical well-being amongst academics was lower during the SARS-CoV-2 measures. The results of a hierarchical regression suggest that decline in physical health is associated with an increase in tasks at home, sickness, less options to plan work and breaks, the self-perceived lower quality of teaching and research and the fear that the measures create a backlog at work. Furthermore, having kids had a negative effect on the work/private life balance, which in turn had an effect on physical well-being. A decline in mental well-being was associated with a fading boundary between work and private life, the necessity to take on more house-keeping tasks, sickness, the fear that the disruptions would create a backlog at work, less control over the work planning and less periods of pause during work.