The association of physical and psychosocial risk factors and musculoskeletal discomfort of 135 Filipino Industrial Engineering students in the remote learning set-up was investigated. Results showed that most of the students were experiencing discomfort in the neck and lower back and more than half recorded discomfort on the upper back, right wrist, hips/buttocks, and right shoulder. There is a moderate correlation between the average study hours per day of the students and the body discomfort score, and a moderate correlation of emotional demand and mental health with body discomfort score, and quantitative demand and low back discomfort score. The study has identified the importance of proper ergonomic setting of the students’ study space, as well as active role of teachers, departments and institutes, and family to implement strategies that will address the significant factors to musculoskeletal discomfort of students.