In reaction to the COVID-19 pandemic, restrictive policies altered student-athletes’ academic and athletic life. Sparse research has investigated the pandemic’s effect on student-athlete mental health in terms of both negative (e.g., depression, anxiety) and positive (e.g., well-being, quality of life) dimensions. This study explored the effect of the COVID-19 pandemic on well-being and quality of life among National Collegiate Athletic Association Division I student-athletes at different stages of their collegiate career. Ninety-nine student-athletes (M age = 19.7 years, SD = 1.5) completed assessments on their mental health. Regression analysis revealed experiences directly related to COVID-19 did not affect general well-being or quality of life, but anxiety, depression, and significant insomnia did. Social well-being was lower for student-athletes closer to graduation (e.g., juniors, seniors), independent of reported anxiety and depression levels. These findings highlight the importance of psychosocial support, particularly in times of crisis, and indicate that tailored support might be beneficial at later stages of the collegiate years.