Wild bees are key witnesses of landscape transformations. Despite a prolific literature on bee conservation, the impact of urbanization on their communities remains unclear, with highly context-dependent results. This limited understanding is aggravated by the fact that few studies have formally examined the impact of diversity indices on their analyses. We addressed this gap by analyzing more than 6,000 specimens across 91 sites, including protected areas, within a highly anthropized landscape. We found that urbanization increased abundance-based diversity indices while simultaneously reducing the richness of threatened species, which only benefited from flower-rich grasslands. This discovery could clarify conflicting results of previous studies, revealing that the decline of threatened species in urban areas may be overshadowed by diverse communities of abundant species. Moreover, we reveal that the existing network of protected areas may not be able to mitigate this decline, as most reserves were dominated by unsuitable forested environments.