Tropical agricultural landscapes can support biodiversity, including forest spill-over species, shaped by habitat factors operating at multiple scales. Understanding these factors is crucial for conserving biodiversity and maintaining ecosystem services. Using mist-netting data, this study examined how land-cover changes influence understorey birds and identified key factors at stand- and landscape-levels, along with a site-specific feature, affecting bird assemblages in agroforestry orchards, rubber tree, and oil palm plantations in Peninsular Malaysia. We captured 39 species over 9,900 netting hours, with forest-associated species comprising 33% of the total. Agricultural type emerged as primary driver of bird diversity, with agroforestry orchards supporting greater species richness and abundance. Canopy cover negatively influenced species richness, total abundance, and the occurrence of carnivorous/insectivorous and granivorous/frugivorous birds. Understorey vegetation height positively impacted bird total abundance. Elevation negatively influenced bird abundance and the occurrence of omnivores but positively affected forest-associated species. Distance to forest was negatively correlated with bird abundance and the occurrence of omnivorous birds. Our findings highlight agroforestry orchards as avian refuges and biological corridors that enhance landscape connectivity and ecosystem functioning in agricultural areas. Specifically, in our region, dense canopy cover in monoculture plantations reduced bird richness and abundance, likely due to reduced sunlight suppressing understorey vegetation and limiting resource availability. Conversely, agroforestry orchards with more open canopy and structurally complex vegetation supported a greater diversity of feeding guilds, including certain forest-associated species. These results underscore the importance of managing tropical farmland by maintaining understorey growth, increasing canopy heterogeneity, and reducing isolation from forest remnants.