Introduction: Medical schools throughout the world were forced to modify their programming during the COVID-19 pandemic. In Malaysia, virtual learning plans were implemented for non-clinical programming, while clinical posting modifications were designed to meet local SOPs. The prolonged enforcement of these modifications to undergraduate medical education will have affected student experiences, including well-being. Since these feelings can relate to perceived relatedness, autonomy, and competence, it is important to identify any potential factors that may lead to reduced intrinsic motivation in students. It is also important to consider how demographic features may contribute to student perspectives, which can be studied using the unique diversity represented by Malaysian students.Methods: A quantitative survey was distributed to Malaysian medical students to assess their overall wellbeing, autonomy in educational decision making, student experiences, and position on changes to graduation timing. Intrinsic components were identified using Principal Component Analysis and were aligned with the three needs for self-determination, namely relatedness, autonomy, and competence. Finally, trends in responses for participants from various sub-populations were assessed using ANOVA testing. Results: Responses were collected from 442 students representing 23 accredited Malaysian medical schools. Upon validation and reliability testing, eight components were identified with themes relating to: mental health, social concerns, communication, timing of modifications, depth of learning, and student-centred learning. Of these, gender was related to mental health, student-centred learning, and delayed graduation, while stage was related to student-centred learning and delayed graduation in addition to concerns about depth of learning and timing of modifications. Interestingly, ethnicity was related to differences in opinions about delayed graduation and income was related to social concerns. Conclusion: The results of this study indicate that, while students were satisfied in general with the content and delivery of their programmes given the circumstances, there is evidence to suggest negative effects on emotional wellbeing, expression of student voice, due to the modifications that were made. Additionally, these feelings related to the three motivational needs, suggesting that students were experiencing a dampened motivational profile during the pandemic. Further, motivational profiles were distinct between student sub-groups, providing insight for developing appropriate and inclusive accommodations moving forward.