The COVID-19 quarantine has caused significant changes in everyday life. This study aimed to evaluate the effect of the quarantine on dietary, physical activity and alcohol consumption habits of Lithuanians and the association between health behaviours and weight changes. An online cross-sectional survey was carried out among individuals older than 18 years in April 2020. The self-administered questionnaire included health behaviour and weight change data. Altogether 2447 subjects participated in the survey. Almost half of the respondents (49.4%) ate more than usual, 45.1% increased snacking, and 62.1% cooked at home more often. Intake of carbonated or sugary drinks, fast food and commercial pastries decreased, while consumption of homemade pastries and fried food increased. A decrease in physical activity was reported by 60.6% of respondents. Every third (31.5%) respondent, more often those already with overweight, gained weight. Multivariate logistic regression analysis showed that the higher odds of weight gain were associated with females, older age, increased consumption of sugary drinks, homemade pastries and fried food, eating more than usual, increased snacking, decreased physical activity and increased alcohol consumption. Our data highlighted the need for dietary and physical activity guidelines to prevent weight gain during the period of self-isolation, especially targeting those with overweight and obesity.