Global decline of pollinators, especially bees, has been documented in many countries. Several causes such as land-use change and agricultural intensification are reported to be the main drivers of the decline. The objective of this study was to investigate the effect of land use on honey bee and stingless bee populations. Research was conducted in Bogor and Malang to compare between two different geographical areas. Managed bees such as honey bees (Apis cerana and A. mellifera) and stingless bees (Tetragonula laeviceps) were investigated to examine the effect of agricultural intensification. Field experiments were conducted by placing beehives in selected habitats (i.e., beekeeper gardens, forests areas, and agriculture areas). Population growth and neonicotinoid residue analysis of bees in different hive locations were measured to study the effect of habitat type. Population growth of bees represents the forager abundance and colony weight. Based on the analysis, we found that habitat type affected forager abundance and colony weight of honey bees (p < 0.05), although the patterns were different between species, region, as well as season. Forests could support the stingless bee colony better than agriculture and home garden habitats. Insecticide (neonicotinoid) was barely recorded in both honey bees and stingless bees.