Equity, diversity, and inclusion remain a prominent focus in medical schools, yet the phenomenon of "belonging" has arguably been overlooked. Little is known regarding how belonging is experienced by medical students from groups that face systemic oppression and exclusion. We employed a sequential explanatory mixed methods design to explore how students from equity-deserving groups (EDGs) experience belonging during medical school, including those who are women, racialized, Indigenous, disabled, and 2SLGBTQIA+. First, we conducted a national cross-sectional survey of medical students (N = 480) measuring four constructs: belonging, imposter syndrome, burnout, and depression. Belonging scores were overall lower for students from EDGs and, more specifically, significantly lowest amongst racialized students. Structural equation models show that poor sense of belonging precedes imposter syndrome and further exacerbates burnout and depression. Next, we sampled and interviewed students (N = 16) from the EDG whose belonging scores were significantly lowest. Participants described the essence of belonging as being able to exist as one's "true self" while emphasizing feelings of acceptance, comfort, and safety as well as being valued and seen as an equal - yet described how routine experiences of "othering" inhibited a sense of belonging, often due to differences in social identity and structural privilege. Poor sense of belonging negatively affected learners' well-being and career trajectory. We illuminate the range of psychological and professional consequences associated with diminished sense of belonging and highlight the need to expand traditional notions of equity, diversity, and inclusion to consider structural barriers to well being.