High-intensity farming can lead to non-random local extinctions and functional filtering of pollinating insect assemblages, disproportionately harming species with certain traits. This process can ultimately reshape pollinator–plant interaction networks in predictable, consistent manners, although this pathway remains largely unexplored. Here, we investigate how agricultural intensification affects the structure of bee–plant interaction networks both directly and indirectly by influencing the functional composition and diversity (in terms of foraging and nesting traits) of the bee assemblages. We considered 24 paired olive farms with contrasting management over a gradient of landscape complexity. We characterized the network structure and functional composition of bee assemblages visiting floral patches in the olive fields by using both functional identity and diversity metrics. We then built Bayesian multilevel models to assess the direct and indirect (via functional filtering processes) effects of agricultural intensification on network properties. We found that most of the effects of agricultural intensification on bee–plant network properties in floral patches occur through the filtering of the bee functional traits. However, while the effects of farming practices occur fundamentally through the filtering of foraging traits, the landscape effects occur via the modification of the nesting guilds. High-intensity herb cover management negatively affected larger bees (also highly correlated with longer proboscis), resulting in a decrease in the overlap of bees' interaction niches. This filtering was mitigated in flowering patches with higher floral cover, which increased the functional diversity of bees, ultimately reducing the overlap of the plants' interaction niches. In turn, the loss of semi-natural habitats in the landscape disproportionately favored ground excavators, causing homogenization of nesting guild composition. This, coupled with decreased floral abundance (patch scale), led to less diverse and structurally simpler networks. In conclusion, our study suggests that agricultural intensification reshapes bee–plant networks in olive landscapes through functional filtering of bee assemblages and provides cues to mitigate these effects. On a small scale, floral patches with abundant flowers buffer the filtering of bees' foraging traits, suggesting that well-managed flower patches help mitigate the functional depletion imposed by agricultural intensification. Meanwhile, favoring semi-natural remnants at a large scale attenuates the homogenization of nesting guild composition.