The association between the changes in lifestyle during coronavirus disease 2019 (COVID-19) confinement and body weight have not been studied deeply. Therefore, the aim of the present study was to determine lifestyle changes, such as eating habits and physical activity (PA) patterns, caused by confinement during the COVID-19 pandemic and to analyze its association with changes in body weight. Seven hundred participants (women, n = 528 and men, n = 172) aged between 18–62 years old of the Chilean national territory participated in the study. Food habits, PA, body weight, and sociodemographic variables were measured through a survey in May and June 2020. The body weight increase presented positive association with the consumption of fried foods ≥ 3 times per week (OR; 3.36, p < 0.001), low water consumption (OR; 1.58, p = 0.03), and sedentary time ≥6 h/day (OR; 1.85, p = 0.01). Conversely, fish consumed (OR; 0.67, p = 0.03), active breaks (OR; 0.72, p = 0.04), and PA ≥ 4 times per week (OR; 0.51, p = 0.001) presented an inverse association with body weight increase. Daily alcohol consumption (OR; 4.77, p = 0.003) was associated with PA decrease. Food habits, PA, and active breaks may be protective factors for weight increase during COVID-19 confinement.