Abstract Background How landscape modifications affect functional diversity of floral characteristics pertinent to pollinators is poorly known. Flowers possess functional traits that sometimes coevolved with pollinators, crucial for the maintenance of both pollinator and plant communities. We evaluated how richness and functional diversity of available understory flowers respond to forest cover and landscape heterogeneity in a multiscale analysis. Plants in bloom were sampled from 25 landscapes in the understory of Atlantic Forest fragments in Brazil. Species were classified into functional groups regarding flower characteristics relevant to pollination. Landscape heterogeneity and forest cover were measured in buffers ranging from 200 to 2000 m from sampling units and their correlation with plant richness and functional diversity was assessed using generalized linear models and further model selection through Akaike’s second-order information criterion. Results Plants’ richness and functional diversity were affected negatively by forest cover. The former responded to forest cover at a regional scale while the latter responded at a local scale. Higher landscape heterogeneity increased richness and functional diversity. Conclusions Our results showed that forest cover and landscape heterogeneity are important to support biodiversity related to pollination, mostly due to the availability of diversified resources and nesting sites associated to different land-uses for pollinators and flowering plant communities. These findings should highlight, along with forest cover, landscape heterogeneity as an environmental management priority in rural tropical areas for mitigating the loss of plant biodiversity and enhancing ecosystem functioning.