Many studies have highlighted the impact of lockdowns on the lifestyle of university students. We do not, however, know how these lifestyles have changed over the course of the COVID-19 pandemic. The objective of the present study was to describe changes in the levels of physical activity, sedentary behaviors, and alcohol consumption in French university students during different periods of the pandemic. This cohort study was conducted between 23 April and 11 December 2020. Measurements were performed four times: Twice during two successive lockdowns and twice during the intervening period. A total of 1294 university students were initially included, and 91 students completed the four measurement points over a seven-month period. Alcohol consumption, physical activity, and sedentary behaviors were measured. The results revealed high levels of physical activity during the first lockdown, but a subsequent decline during the pandemic that was partly explained by time. The pandemic had a positive effect on alcohol consumption. Sedentary levels were higher during both lockdowns, and sedentary behaviors tended to persist over time. This study raises concerns about the long-term effects of the pandemic on students’ health and lifestyle. The preponderance of distance learning should be reconsidered, given the negative impact of physical inactivity and sedentary behavior on long-term health, especially in young adults.