Indigenous peoples and local communities (IPLC) historically have cultural practices and knowledge related to plants. These groups often live in rural areas, far from urban centers. However, due to urban expansion and migratory movements from rural to urban areas, many IPLC currently live in or nearby cities, where urban contexts can pose a challenge for their adaptation. Based on case studies in Santa Catarina (Brazil), we assessed the role of urban, peri-urban and rural home gardens for agrobiodiversity conservation in local communities. Home gardens managed by traditional farmers, Polish descendants, as well as Afro-descendant communities (Quilombolas), share the characteristic of functioning as dynamic agrobiodiversity repositories. Among these three groups, urban home gardens are vital to their owners for maintaining agrobiodiversity and related cultural practices, while in rural contexts the home garden is part of a broader plant management system. We registered about 620 species of plants present in 192 home gardens, of which 300 of them are native from Brazil. Among these 300 native species, 64 were recorded in at least two of the case studies. For some species, such as manioc, home gardens also contribute to maintaining the genetic diversity of plant populations. These results reinforce traditional communities’ roles in maintaining their home gardens as an important place for in situ conservation of agrobiodiversity and for their cultural reproduction, even in urban contexts.