A catastrophic disaster may cause distant health impacts like immobility and obesity. The aim of this research was to analyse the association of the COVID-19 pandemic and lifestyle factors -exercise habit and overweight status in the Japanese population. Nation-wide online questionnaires were conducted five times from October 2020 to October 2021. The changes in exercise habit, body mass index (BMI) and overweight status (BMI >25kg/m2) were compared between the first questionnaire and a questionnaire conducted a year later. Risk factors for losing exercise habit or becoming overweight were analysed using multiple regression. Data were obtained from 16,642 participants. In the early phase of the pandemic, people with high income and elderly females showed a higher risk for decreased exercise days. The proportion of overweight status increased from 22.2% to 26.6% in males and from 9.3% to 10.8% in females. Middle-aged males, elderly females, and males who experienced SARS-CoV-2 infection were at higher risk of becoming overweight. Our findings suggest that risks for immobility and overweight are homogeneous. Continuous intervention for elderly females and long-term intervention for males infected with SARS-CoV-2 might be especially needed. As most disasters can cause similar social transformation, research and evaluation of immobility and obesity should address future disaster preparation/mitigation plans.