The inselbergs ecosystem constitutes isolated rocky granite or gneiss outcrops, as terrestrial habitats islands, that emerge abruptly from their surrounding ecosystems, such as savannah and forests. They are characterized by extreme edaphic and microclimatic conditions, such as the scarcity of water and nutrients in the soil, few alternatives for fixing roots, seeds, and propagules, in addition to excessive exposure to wind, light, and abrupt daily thermal variation. Typically, old, climatically buffered, infertile landscapes (OCBILs) as inselbergs are hypothesized to be rich in species and endemics, low dispersability, and high clonality in many plants, as well as reduced extinction, marked palaeoendemism, small isolated populations, and adaptations to low-fertility soils. The combination of all these attributes has been a challenge for the understanding of patterns of taxonomic, ecological, climate, and biogeographical, restoration and conservation biology studies. Despite its importance in biodiversity, inselbergs are one of the more neglected and threatened ecosystems, which raises the urgency for conservation priority plans due to the current fast global climate and land-use change scenario. Thus, this study aims to understand the ecological process related to taxonomic, functional, and phylogenetic diversity of species at inselberg ecosystems, as well as evaluate the effects of climate change by ecological niche models and estimate the effects of geographic isolation on the phylogenetic diversity of plants through landscape connectivity models, to generate studies that can understand the rupicolous ecosystems associated with Brazilian Neotropical inselbergs and thus contribute to the maintenance and conservation of these ecosystems. Our results indicating differences in plant community structure and diversity among local and regional scale reveal higher taxonomic and functional β-diversity driven by higher taxonomic and functional turnover component, exhibits highly stress-tolerant and conservative functional strategies (CSR) showing the effect of environment on functional traits, extreme loss of suitable area, where all scenarios showed range contraction that can achieve losses up to 86.7% in the next 50 years and greater isolation between the northeastern and southeastern inselbergs core areas reflecting the joint-effect of isolation by resistance and environmental filtering. This pattern can create more isolated communities, composed by less phylogenetic diversity of closer species and functionally adapted to environmental conditions (impoverished soils andbuffered climate), supporting the OCBIL theory. Therefore, the ecological process that shapes the community assembly is linked to the scale effect, the pattern of taxonomic and functional β-diversity could result from a strong niche filtering process, while environmental-trait approach, functional strategies, and habitat suitability are drives by environmental filtering. On a landscape scale, the effect of biogeographical isolation is added to environmental filtering in inselberg ecosystems. We highlighting that the conservation strategies should be directed towards the protection of endemic and/or threatened species and the creation of protected areas with a focus on protecting mainly isolated inselbergs, as well as groups from each of the core areas. Finally, the implementation of mitigating actions through effective restoration strategies that minimize the effect of isolation between the central areas, and that take into account the maintenance of different phylogenetic lineages and the evident specializations of species for microhabitats of inselbergs. Keywords: Rock outcrop. Beta diversity. Functional traits. Landscape resistance. Connectivity. Biodiversity conservation. Atlantic Forest. Caatinga