Aim: The COVID-19 pandemic has led to adaptation in teaching and learning methods. There is a possibility that this shift from the classroom to online learning will persist post-pandemic with implications to all involved. We explored the contribution of personal, academic stressors and environmental factors contributing to musculoskeletal pain among undergraduates due to online learning by integrating data from an online survey and one-to-one in-depth interviews. The association between musculoskeletal pain, personal, academic stressors and environmental factors among undergraduates due to online learning was also investigated. Methods: Both quantitative and qualitative methods were used. A questionnaire was completed by 179 undergraduates (34 males and 145 females) aged between 18 to 25 years old. This was followed by an online, in-depth, one-to-one interview among 10 female undergraduates who reported severe musculoskeletal pain. The two sets of findings were integrated using a triangulation protocol. Result: The three most common musculoskeletal pains experienced by undergraduates due to online learning were low back (73.2%), followed by neck (68.7%) and shoulder (58.7%) pain. The six main themes identified from the interviews were: (1) Musculoskeletal pain characteristics; (2) academic issues; (3) difficulties faced by undergraduates due to teaching and learning; (4) emotions towards work/study; (5) work environment; and (6) time spent working at a workstation. Upper back pain was identified to be associated with personal (p < 0.05) and most environmental factors (p < 0.05). From the triangulation model, it was shown that personal, academic stressors and environmental factors were mainly from the workstation, uncomfortable environment, working posture and time spent at the workstation, which all contributed to musculoskeletal pain. Conclusions: This study showed that exercise, academic stressors, and environmental factors were associated with musculoskeletal pain among undergraduates due to online teaching and learning sessions. There may be a need to integrate an online prevention of musculoskeletal pain education package based on a biopsychosocial model with online teaching and learning for undergraduates.