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The aim of the study was to analyse health-related quality of life (HRQoL) among the Estonian general population and its socio-demographic and behavioural correlates during the COVID-19 pandemic. Longitudinal data on 1781 individuals from an Estonian rapid-assessment survey on COVID-19 were used. HRQoL was assessed with the EQ-5D-3L in June 2020 (baseline) and in May 2021 (follow-up). The HRQoL index score and its socio-demographic and behavioural variations were analysed using paired t -tests and Tobit regression modelling. Statistically significant declines in mean EQ-5D index scores were observed for all socio-demographic and behavioural variables considered. Most of these changes were due to increased reporting of problems in the pain/discomfort and anxiety/depression health domains. Older age, being unemployed or economically non-active and having financial difficulties were significantly associated with lower HRQoL in both baseline and follow-up measurements. In the follow-up data, women had significantly lower HRQoL compared to men, whereas higher education proved to be the only protective factor regarding HRQoL. Unhealthy dietary habits and low physical activity had a negative impact on the HRQoL score in the follow-up data. These results indicate that the COVID-19 pandemic has had a substantial impact on HRQoL in the Estonian population.