The consequences of the COVID-19 pandemic period on a nation’s well-being remain inadequately understood, especially over time. Therefore, this research aims to map the changes in the subjective well-being (SWB) of the general Belgian adult population during the COVID-19 pandemic. Analyses of variances (ANOVA) were performed to evaluate the changes in SWB during the pandemic at five different time points during the period from February 2020 until December 2022 using repeated cross-sectional representative samples of the Belgian population. The differences over time in subjective well-being were investigated in terms of life evaluation, positive affect, and negative affect. The changes in autonomy, competence, relatedness, loneliness and peace of mind were also explored as explanatory variables. Moderation analyses were performed to investigate the differential changes in well-being for different age groups. Our results show the subjective well-being of the Belgian population decreased during the COVID-19 pandemic, notably during the second lockdown and the fifth wave. Furthermore, younger individuals are significantly more susceptible to negative changes in well-being during the pandemic period. Finally, our results show that peace of mind is an important predictor of all SWB components during the pandemic. Based on these results several policy recommendations are formulated.