Abstract Aim Habitat loss and alteration are widely considered one of the main drivers of current pollinator diversity loss. Yet little is known about habitat importance and preferences for major groups of pollinators, although this information is crucial to anticipate and mitigate the current decline of their populations. We aim to rank and assess the importance of different habitats for bees, to determine the preference for and avoidance of particular habitat types by different bees and to quantify the diversity of bees within and among habitats. Location North‐eastern USA. Time period The sampling was done over 15 years (2001–2015). Major taxa studied Apoidea. Methods We used an unprecedented extensive dataset of >15,000 bee specimens, comprising more than 400 species collected across north‐east USA. We extracted habitat information from the sample points and used network analyses, null models comparisons and beta‐diversity analysis to assess habitat importance, habitat preference, use and diversity. Results We found that natural habitats sustain higher bee diversity and a different set of species than agricultural and urban areas. Although many bee species used human‐altered habitats, most species exhibited strong preferences for forested habitats and only a few preferred altered habitats over more natural habitats. In contrast to previous studies, landscape composition only had moderate buffer effects on diversity loss. The loss of biodiversity in human‐altered environments could have been higher but it was partially compensated by the presence of human commensals and exotic species. Main conclusions Although human‐altered environments may harbour a substantial number of species, our work suggests that preserving natural areas is still essential to guarantee the conservation of bee biodiversity.