Background: When the first cases of COVID-19 (caused by SARS-CoV-2 virus infection) were discovered, exceptional norms to fight the spread of the virus were established by applying movement restrictions (lockdown) in many countries. These unprecedented norms led to sedentary behaviours and less healthy diets which could persist for much longer after lockdown. The aim of this study was to analyse the physical activity, eating habits, self-perceived well-being, and toxic habits, as well as the perceived changes of these habits with respect to the pre-pandemic period, in a population of university students in the second year of the COVID-19 pandemic. Methods: A single-centre, cross-sectional study was conducted in a population of university students of healthcare degrees. A total of 961 students (639 (66.5%) women and 322 (33.5%) men) signed the informed consent and completed the questionnaire. The study was conducted through an anonymous survey, which was voluntarily self-completed by the students on an online platform. The questionnaire was based on the Spanish Health Survey and it was divided into six main parts: demographic and anthropometric characteristics, physical activity, eating habits, well-being measures (sleeping habits, health state, and stress), toxic habits, and perception of the influence of the COVID-19 pandemic on the variables described. Results and conclusions: The results showed that, during the second year of the pandemic, statistically significant dependence was identified for those students that showed higher levels of physical activity with greater perceived physical activity (p< 0.05), healthier eating habits (p< 0.05), and a better self-perceived health state (p< 0.05), with respect to the 12 months before the COVID-19 pandemic. On the other hand, there was a negative correlation between the sedentary students and greater perceived physical activity (p< 0.05). With regard to toxic habits and physical activity, a significant correlation was only detected between sedentary behaviour and cocaine consumption (p< 0.05). Analysing eating habits, it was observed that the students who smoked, consumed alcohol, and binge drank had low adherence to the Mediterranean diet (p< 0.05). In addition, those students with high stress levels slept less than 7 h (p< 0.05).