The Conséquences de la pandémie de COVID-19 sur la santé mentale des étudiants (COSAMe) survey was conducted among university students in France during the COVID-19 pandemic and found that although there was a slight decrease in anxiety, depression, and stress between the first lockdown (T1) and 1 month after it ended (T2), the prevalence of suicidal ideation had increased between these periods and 1 in 5 students had probable posttraumatic stress disorder (PTSD) at T2. These results emphasize the need to explore the long-term consequences of the COVID-19 pandemic. To measure the prevalence of mental health symptoms among university students in France 15 months after the first lockdown (T3) and to identify factors associated with outcomes. This cross-sectional study reports data from the third measurement time of the repeated COSAMe survey, which took place from July 21 to August 31, 2021, through an online questionnaire sent to all French university students. The prevalence of suicidal thoughts, PTSD (PTSD Checklist for the Diagnostic and Statistical Manual of Mental Disorders [Fifth Edition] [PCL-5]), stress (Perceived Stress Scale), anxiety (State-Trait Anxiety Inventory), and depression (Beck Depression Inventory) at T3 were gender- and degree-standardized and compared with prevalence rates at T1 and T2. Multivariable logistic regression analyses identified risk factors. A total of 44 898 students completed the questionnaires. They were mainly women (31 728 [70.7%]), and the median (IQR) age was 19 (18-21) years. Standardized prevalence rates of stress, anxiety, depression, suicidal thoughts, and PTSD were 20.6% (95% CI, 20.2%-21.0%), 23.7% (95% CI, 23.3%-24.1%), 15.4% (95% CI, 15.1%-15.8%), 13.8% (95% CI, 13.5%-14.2%), and 29.8% (95% CI, 29.4%-30.2%), respectively. Compared with the decreased prevalence rates at T2, there was an increase at T3 for stress (2.5% increase), anxiety (13.9% increase), and depression (22.2% increase). The prevalence of suicidal ideation continued to increase from T1 (10.6%) to T3 (13.8%), and the prevalence of probable PTSD increased from 1 in 5 students to 1 in 3 students between T2 and T3. Female and nonbinary participants; participants without children and living in an urban area; and those with financial difficulties, a chronic condition, psychiatric history, COVID-19 history, social isolation, and low perceived quality of information received were at risk of all poor outcomes at T3 (eg, stress among women: adjusted OR, 2.18; 95% CI, 2.05-2.31; suicidal thoughts among nonbinary respondents: adjusted OR, 5.09; 95% CI, 4.32-5.99; anxiety among students with children: adjusted OR, 0.68; 95% CI, 0.56-0.81; depression among students living in a rural area: adjusted OR, 0.80; 95% CI, 0.75-0.85). These results suggest severe long-lasting consequences associated with the pandemic on the mental health of students. Prevention and care access should be a priority.