© 2018 John Wiley & Sons Ltd Aim: We examined the effects of space, climate, phylogeny and species traits on module composition in a cross-biomes plant–hummingbird network. Location: Brazil, except Amazonian region. Methods: We compiled 31 local binary plant–hummingbird networks, combining them into one cross-biomes metanetwork. We conducted a modularity analysis and tested the relationship between species’ module membership with traits, geographical location, climatic conditions and range sizes, employing random forest models. We fitted reduced models containing groups of related variables (climatic, spatial, phylogenetic, traits) and combinations of groups to partition the variance explained by these sets into unique and shared components. Results: The Brazilian cross-biomes network was composed of 479 plant and 42 hummingbird species, and showed significant modularity. The resulting six modules conformed well to vegetation domains. Only plant traits, not hummingbird traits, differed between modules, notably plants’ growth form, corolla length, flower shape and colour. Some modules included plant species with very restricted distributions, whereas others encompassed more widespread ones. Widespread hummingbirds were the most connected, both within and between modules, whereas widespread plants were the most connected between modules. Among traits, only nectar concentration had a weak effect on among-module connectivity. Main conclusions: Climate and spatial filters were the main determinants of module composition for hummingbirds and plants, potentially related to resource seasonality, especially for hummingbirds. Historical dispersal-linked contingency, or environmental variations not accounted for by the explanatory factors here evaluated, could also contribute to the spatial component. Phylogeny and morphological traits had no unique effects on the assignment of species to modules. Widespread species showed higher within- and/or among-module connectivity, indicating their key role connecting biomes, and, in the case of hummingbirds, communities within biomes. Our results indicate that biogeography and climate not only determine the variation of modularity in local plant–animal networks, as previously shown, but also affect the cross-biomes network structure.