Objective COVID-19 forced third-level students to transition to online learning (OL). Many students encountered issues with OL, such as accessibility. However, the relationship between OL issues and mental health during this time remains poorly understood. Participants: Third-level students in Ireland (N = 268) completed an online questionnaire examining experiences with OL and mental health during COVID-19. Methods: OL social, lecturer, accessibility, individual skills, and environment issues, were entered into logistic regression analyses to examine whether these variables predicted mental health outcomes and/or preference to keep OL. Results: Students reporting more individual skills issues were more likely to attain a probable diagnosis of posttraumatic stress disorder, complex posttraumatic stress disorder, and depression (p < 0.0083); students who reported more environment issues were less likely to report preference to keep OL (p < 0.0005). Conclusions: Given individual skills issues associated with worse mental health, future research should examine improving student perceptions of their own OL skills.