The objective of this research was to study the relationship between the body weight and diet, physical activity, and other habits among freshmen students by sex, and to determine whether these habits have changed during the post-era of the COVID-19 pandemic. A serial cross-sectional study with data from 11 Spanish universities was carried out. In total, 10,096 first-year university students (73.2% female, mean age = 19.0 ± 1.5 years) completed an online self-administered questionnaire between 2012 and 2022. For some analyses, questionnaires were categorized by the year in which the survey was filled out as Before COVID-19, Lockdown, and New Normal. In total, 72.9% of participants were within the normal weight range, and 17.7% of men and 11.8% of women were overweight (p< 0.001). The students who did not meet the WHO criteria of physical activity, spent more than 7 h per day sitting, and skipped breakfast had a higher prevalence of obesity (p< 0.05). According to the period of study, the prevalence of overweight/obesity Before COVID-19 was 16.1% (95% CI: 15.4–16.9%), while in Lockdown the prevalence was significantly higher (20.2, 95% CI: 17.1–23.8) and in New Normal it was 18.9% (CI: 15.7–22.5). Moreover, the study suggests that during the Lockdown period, there was a reduction in the practice of physical activity and an increase in the prevalence of a healthy diet. For all these, it is necessary to propose public health interventions that improve the lifestyles of university students.