This cross-sectional study determined the appreciation of the learning environment and development of higher-order learning skills among students attending the Medical Curriculum at the International Medical University, Malaysia which provides traditional and e-learning resources with an emphasis on problem based learning (PBL) and self-directed learning. Of the 708 participants, the majority preferred traditional to e-resources. Students who highly appreciated PBL demonstrated a higher appreciation of e-resources. Appreciation of PBL is positively and significantly correlated with higher-order learning skills, reflecting the inculcation of self-directed learning traits. Implementers must be sensitive to the progress of learners adapting to the higher education environment and innovations, and to address limitations as relevant.