The study aimed to describe the association between internal migration status and QoL in medical students from a Peruvian university. A cross-sectional survey was conducted in medical students from a public university in Lima, Peru. We used the brief version of the World Health Organization Quality of Life instrument (WHOQOL-BREF) and obtained data on demographic and migration-related student’s characteristics. Linear mixed models were used to assess how migration status affected each of the WHOQOL-BREF domains (physical health, psychological status, social relationships, and environment). Of 410 participants, 110 (27%) and 46 (11%) were ‘late’ and ‘recent’ migrants, respectively. Compared with non-migrants, most recent migrants were older (87.0%, p = 0.000), lived alone (32.6%, p = 0.000), had at least one highly educated parent (87.0%, p = 0.002) and reported no chronic conditions (73,9%, p = 0.019). The environment domain scored the lowest and the psychological domain, the highest. Adjusting by all study confounders, migration status was not associated with QoL in any domain. However, adjusting by variables showing a favorable proportion in migrants (parental education and chronic conditions), recent migrants had lower QoL than did non-migrants in the environment domain (b − 4.8, 95% CI −9.2 to −0.5). The results suggest that the parents’ higher education level and the absence of chronic conditions could protect migrants’ QoL against environmental stressors.