Due to COVID-19, the sporting season at Canadian post-secondary institutions was cancelled in March 2020. It is unclear how student-athletes managed their training at home when social distancing and lockdown (SD/L) policies were in place and what barriers they encountered. Our cross-sectional study of 433 student-athletes examined (a) how athletes adapted their training routines, (b) what barriers they experienced to maintain their training, (c) whether different motivational profiles were associated with differences in training behaviours and mental health, and (d) what variables predicted athletes' motivation to train during this prolonged offseason. Student-athletes across Canada were recruited to complete an online survey between August and September 2020. Results showed that athletes significantly reduced their training load and intensity, with approximately 25% exercising two or fewer days a week. Barriers to training included limited access to fitness resources and equipment, inconsistent training routines, and experiencing emotional distractions, some of which were significantly greater for female athletes compared to male athletes. For motivation profiles, athletes with higher levels of intrinsic motivation maintained the intensity of their workouts and experienced lower mood disturbance. A hierarchical multiple regression revealed that being male, being younger, having higher levels of intrinsic and introjected motivation, having access to fitness resources, having fewer irregular training routines, having fewer emotional distractions, and lower mood disturbance were significant predictors to being motivated to train during the pandemic. We discuss strategies coaches and trainers can implement to best support their student-athletes during stressful times.