Context Island Biogeography Theory and Habitat Amount Hypothesis postulate species richness and densities to increase with connectivity and habitat amount, while niche theory highlights the importance of environmental heterogeneity for species coexistence. Additional ecological niches in heterogeneous landscapes increase species richness and functional and phylogenetic diversity, but larger, less isolated habitats are expected to enlarge species densities by mass effects without effects on functional or phylogenetic diversity. Objectives We assessed the relative contribution of habitat amount, isolation and environmental heterogeneity on taxonomic, functional and phylogenetic diversity of the particular canga vegetation, i.e., rupestrian savannas associated to banded ironstone outcrops from the Carajás Massif, Eastern Amazon. Methods We sampled vegetation at 48 sampling points comprising different physiognomies from 5  canga patches. Diversity measures were modelled as response variables in linear mixed models, using non-collinear predictors of habitat amount, isolation and environmental heterogeneity. Results Diversity and species composition differed among canga physiognomies, indicating that environmental filters segregate canga plant metacommunity in physiognomy-specific species pools. Landscape roughness, a proxy for heterogeneity on the landscape level, increases species densities and functional richness. Additionally, habitat amount was positively associated with the degree of phylogenetic relatedness and functional diversity in communities. Conclusions Our results suggest that configurational landscape heterogeneity increases the number of available ecological niches, while larger habitat amounts select for functionally and phylogenetically convergent species. These different underlying mechanisms need to be considered for management plans and reserve design for canga ecosystems, so that functional canga portions can be protected.