Biodiversity persistence in non-woody tropical farmlands is poorly explored, and multi-species assessments with robust landscape-scale designs are sparse. Modeled species occupancy in agricultural mosaics is affected by multiple factors including survey methods (convenience-based versus systematic), landscape-scale agriculture-related variables, and extent of remnant habitat. Changes in seasonal crops can additionally alter landscape and habitat conditions thereby influencing species occupancy. We investigated how these factors affect modeled occupancy of 56 resident bird species using a landscape-scale multi-season occupancy framework across 24 intensively cultivated and human-dominated districts in Uttar Pradesh state, north India. Convenience-based roadside observations provided considerable differences in occupancy estimates and associations with remnant habitat and intensity of cultivation relative to systematic transect counts, and appeared to bias results to roadside conditions. Modeled occupancy of only open-area species improved with increasing intensity of cultivation, while remnant habitat improved modeled occupancy of scrubland, wetland and woodland species. Strong seasonal differences in occupancy were apparent for most species across all habitat guilds. Further habitat loss will be most detrimental to resident scrubland, wetland and woodland species. Uttar Pradesh’s agricultural landscape has a high conservation value, but will require a landscape-level approach to maintain the observed high species richness. Obtaining ecological information from unexplored landscapes using robust landscape-scale surveys offers substantial advantages to understand factors affecting species occupancy, and is necessary for efficient conservation planning.