Understanding how biodiversity is partitioned among alternative land-uses is an important first step for developing effective conservation plans in multiple-use landscapes. Here, we analysed nestedness patterns of species composition for nine different taxonomic groups [dung beetles, fruit-feeding butterflies, orchid bees, scavenger flies, leaf-litter amphibians, lizards, bats, birds and woody plants (trees and lianas)] in a multiple-use forestry landscape in the Brazilian Amazon containing primary, secondary and Eucalyptus plantation forests. A formal nestedness analysis was performed to investigate whether species-poor land-uses were comprised of a subset of species from more diverse forests, and the extent to which this pattern varied among taxa. At the landscape-scale the species-by-sites matrices were significantly nested for all nine taxonomic groups when both sites and species were sorted to maximally pack the species/occurrence matrix and, except for orchid bees when sorted by land-use intensity (primary forest to Eucalyptus plantation). Different patterns emerged when we conducted pairwise analyses of nestedness between the three forest types: (a) most of the taxonomic groups were nested in accordance with increased land-use intensity; (b) neither orchid bees nor leaf-litter amphibians from secondary forest made up a significant nested subset of primary forest species, although species found in Eucalyptus plantation sites were nested within secondary forest communities; and (c) lizards from Eucalyptus plantations were not a nested subset of either primary or secondary forest. Our findings emphasize the complex nature of patterns of species occupancy in tropical multiple-use forestry landscapes, and illustrate that there may be no easy solutions to questions regarding the conservation value of secondary and exotic plantation forests.