The long-term effect of the COVID-19 pandemic on lifestyle changes remains understudied. This cross-sectional study aimed to assess changes in nutrition, physical activity, and body weight among Lithuanian students during the pandemic and their post-pandemic persistence. Data were collected from 1430 first-year students (325 males, 1105 females) through an online self-administered questionnaire. The students indicated an increase in the consumption of snacks, fast food, home-made confectionery, and sweets. A decrease in physical activity during the pandemic was reported by 34.9% of males and 33.2% of females. Lifestyle changes during the pandemic were associated with post-pandemic habits. A higher proportion of females (38.7%) than males (31.1%) indicated an increase in BMI, which was more pronounced among students with overweight. A multivariate logistic regression analysis revealed that reduced physical activity; the increased consumption of red meat, snacks, fast food, and home-made confectionery during the pandemic; and post-pandemic BMI were linked with weight gain. After the pandemic, weight gain persisted in 40.9% of students who continued to follow unhealthy nutrition habits and had reduced physical activity. The study emphasizes that the promotion of a healthy diet and regular physical activity among university students is essential for developing lifelong habits that contribute to a healthy body weight and overall well-being.