The COVID-19 pandemic has significantly impacted daily activities worldwide. University students may have experienced substantial changes in daily living as a result of restrictions on university attendance. The return to normalcy may take a long time, and understanding the influence that shifts in daily routines have had on the lifestyles of university students may inform approaches to support overall well-being. We analyzed changes in the lifestyles of students enrolled at a health sciences university during the COVID-19 pandemic. This longitudinal study took place at the Faculty of Medicine and Nursing in the University of the Basque Country in Spain, and the final sample consisted of 113 nursing students, 109 medical students, and 45 physiotherapy students. Our results demonstrate changes in lifestyles of university students during the pandemic. MedDiet adherence scores and the percentage of students with high adherence increased during the pandemic. This increase was due to the increased consumption of vegetables and nuts. In terms of physical activity, the practice of moderate and intense physical activity was maintained. These results provide important information for both public health authorities and educational institutions to guide strategies to maintain the well-being of students and enhance opportunities for young adults to lead a healthy lifestyle.