This cross-sectional observational study compares the health behaviors of university students in France and Italy, examining how their choices and lifestyles were affected by the COVID-19 pandemic with the aim of contributing to the development of adequate public health and higher education institutions interventions. The French cohort was investigated between January and February 2022, while the Italian cohort was examined between March and April 2022. In both contexts, data were collected through web surveys using institutional directories of university degree programs. Data were collected using standardized tools, validated and recovered in full or partial form. The tool used consisted of three specific sections (general experience, eating habits, physical activity), to which a fourth, dedicated to describing the sociographic picture of the respondents, was added. It was found that the pandemic mainly affected the mental health and sense of well-being of young people in both countries. The pandemic altered dietary habits (41.8% of the French subjects and 38.3% of the Italians declared an increasing of their food intake), alcohol consumption (9.0% of the Italian respondents and 4.0% of the French respondents reported an increased alcohol consumption), propensity to smoke (among the French 85.3% subjects remained non-smokers versus 65.3% of the Italian subjects), sleep quality (25.7% of Italian students 16.6% of French students experienced a decline in the quality of their sleep), and physical activity levels (the percentage of physically active French subjects rose to 72.4%, whereas among Italian students, it dropped to 68,4%). The results emphasize the need for the implementation of relational and psychological interventions, even digital, to face the consequences of social isolation and negative changes in everyday behaviors due to the restrictions during the COVID-19 pandemic.