Abstract Background The COVID-19 pandemic has resulted in a disruption of daily routines and changes in health behaviors leading to widespread concerns about unfavorable changes in weight status and a potential increase in the prevalence of obesity. This study examined the long-term impact of the COVID-19 pandemic on changes in weight status and its possible dependency on educational level and mental health. Methods The study utilizes the Danish Health and Well-being Survey with repeated self-reported information on weight status collected before the COVID-19 pandemic (autumn of 2019) and twice during the pandemic (autumns of 2020 and 2021). Information on educational level was derived from registers, whereas mental health was measured using validated scales. Generalized estimating equations were performed to investigate changes in mean weight and body mass index (BMI) category (BMI < 30 to BMI ≥ 30) between 2019 and 2021 and to investigate potential differences in changes in weight status by pre-pandemic educational level and mental health. Results Mean weight significantly increased by 0.34 kg [95% confidence interval (CI): 0.16–0.51] in 2020 and by 0.46 kg (95% CI: 0.26–0.66) in 2021 compared with pre-pandemic weight status. The increase was greater among individuals with lower educational levels and poorer mental health. There were no significant changes in BMI category during the pandemic. Conclusion The results showed a significant increase in mean weight among the Danish population, particularly among individuals with lower educational levels and poorer mental health, but without detectable differences in obesity, supporting a long-term but minor impact of the COVID-19 pandemic on weight status.