Secondary forests have reclaimed one sixth of deforested land worldwide, and much of this revegetated forest lies in agricultural and increasingly semi-urban landscapes. While, many studies have described faunal populations such as birds across forest-agricultural landscapes, they generally note minor changes in total species richness and more significant changes in species composition. Few studies, however, consider faunal diversity among secondary forests of different management history, such as manual restoration or natural revegetation. In this study, we surveyed bird communities in three forest sites of varying restoration and natural revegetation treatments in a tropical urban-agricultural landscape in the Ecuadorian Amazon. Our sites include manually restored and naturally revegetating forest of 20–40 years since clearing. We found that a diverse assemblage of birds visit and occupy forest fragments within the urban- agricultural landscape, including two IUCN-listed near-threatened species. Bird species richness was similar across sites of different management history; species composition varied only slightly, but differences existed in presence and occupancy for forest-dependent groups, such as large frugivores and forest insectivores. In the manually restored site, bird diversity may have been limited by under-developed forest structure, but we were unable to isolate the effects of patch size and landscape matrix. We suggest that future restoration activities consider forest structure in addition to plant species diversity when attempting to restore faunal populations, and that future studies take heed of landscape and matrix parameters when evaluating restoration projects.