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There is a global concern of pollinator declines and linked ecosystem service losses. However, although land-use changes are a primary threat to biodiversity, how land-use change affects pollinator communities, pollination networks and fruit-set of food crops is poorly understood. The impact of land-use changes is especially understudied in tropical systems, even though most tropical crops are highly dependent on animal pollination. Using 40 sites to investigate diurnal and nocturnal flower visitors in small-scale agroecosystems across land-use gradients in Thailand and tropical South-western China, we show that habitat structure shapes pollinator communities at local (floral species richness) and landscape level (percentage of tree plantation in a 500 m radius and percentage forest in a 5 km radius), influencing both the species richness of pollinators and their visitation rates. These, in turn, alter plant-pollinator network structure: community-level specialization increases with floral species richness and percentage of forest cover. However, the specialization decreases with percentage of tree plantation, illustrating that natural habitat better supports specialized species. Furthermore, fruit-sets of several crops were affected by land-use. Notably, fruit-set of mango was positively associated with the percentage of forest cover in the surrounding landscape. These findings reveal how land-use influence pollinator communities and highlight how natural habitats may safeguard ecosystem services.