The inclusion of carbon stock enhancements under the Reducing Emissions from Deforestation and Forest Degradation (REDD+) framework will likely drive a rapid increase in biosequestration projects that remove carbon from the atmosphere through rehabilitation of degraded primary rain forests. Such projects could also present an important opportunity to reverse losses of biodiversity from degraded rain forests, but concern has recently been expressed that management interventions to increase carbon stocks may conflict with biodiversity conservation. Focusing on a large-scale rain forest rehabilitation project in northern Borneo, we examine: (i) how intensive rehabilitation of selectively logged forests affected patterns of bird community composition and (ii) whether changes in vegetation structure explain observed shifts in avian guild structure and species composition. Bird composition differed between unlogged, naturally regenerating logged, and rehabilitated logged habitats, with the avifauna of rehabilitated forest more similar to that of naturally regenerating forest. Crucially, rehabilitation did not adversely affect either those species that declined after logging or those species that are IUCN Red Listed. Rehabilitation reduced the prevalence of vines and shrubs within regenerating forest, and across all habitats, the abundance and species richness of all birds and of obligate frugivores were positively related to vine prevalence. In contrast, the abundance and richness of frugivore–insectivore generalists and of salliers were negatively related to vines, suggesting that avifaunal responses to forest rehabilitation were attributable to liberation cutting of vines. Management intervention to increase carbon stocks had little adverse effect on avian biodiversity and we therefore argue that rain forest rehabilitation should play a strong role in future REDD+ agreements.