Bacterial pathogens secrete chemically diverse iron chelators called siderophores, which may exert additional distinctive functions in vivo. Among these, uropathogenic E.coli often co-express the virulence-associated siderophore yersiniabactin (Ybt) along with catecholate siderophores. Here we used a novel mass-spectrometric screening approach to reveal that yersiniabactin is also a physiologically favorable copper (II) ligand. Direct mass-spectrometric detection of the resulting Cu(II)-Ybt complex in mice and humans with E. coli urinary tract infections demonstrates copper binding to be a physiologically relevant in vivo interaction during infection. Yersiniabactin expression corresponded to higher copper resistance among human urinary tract isolates, suggesting a protective role for this interaction. Chemical and genetic characterization showed that yersiniabactin helps bacteria resist copper toxicity by sequestering host-derived copper (II) and preventing its catechol-mediated reduction to copper (I). Together, these studies reveal a new virulence-associated function for yersiniabactin that is distinct from iron binding.