BackgroundEthnopharmacological studies about migrants reveal a dynamic process of knowledge and use of medicinal plants. In this study, we sought to elucidate quantitative and qualitatively the main factors influencing the use of medicinal plants by migrants from rural areas to an urban region in Brazil with traces of remnant natural vegetation.MethodsSeven Northeastern individuals who migrated to the Southeastern Region of Brazil (Bororé Peninsula, in the city of São Paulo) were selected to participate in semi-structured interviews regarding the use of medicinal plants throughout their lives, and indicated an inhabitant in their hometown that would be able to accompany the field collections in each area. Socioeconomic, educational, family structure, and use of Western medicine data were provided during interviews with the individuals from their hometowns. Plant samples cited by the interviewees were collected both at the current place of residence and in their hometowns.ResultsThe participants cited 131 plants and 315 recipes, being the main indications related to the gastrointestinal system, respiratory problems, and pain and inflammatory processes. We observed that most plant uses were maintained after migration. Higher percentages of maintenances and incorporations in plant uses occurred to exotic species, while replacements happen mainly to native plants. The introduction of new species into the migrants’ therapeutics occurred mainly by observations of organoleptic similarities between the substituted plant and the incorporated species, conversations with neighbors, and contact with the television and print media. In addition, the public health system allowed the interviewees access to prophylactic drugs, leading to the discontinuation of certain recipes used in endemic diseases.ConclusionMigrants were exposed to information about new plants and their uses, new diseases, and socioeconomic and cultural differences that impacted their use of medicinal plants. Although migration to a more developed city facilitated access to public health and education, on the other hand, it made access to fresh medicinal plants difficult, causing some medicinal plants to be replaced or ceased to be used.Electronic supplementary materialThe online version of this article (10.1186/s13002-018-0270-3) contains supplementary material, which is available to authorized users.