Vancomycin-resistant Enterococcus faecium (VREfm) is a nosocomial pathogen resistant to most antimicrobials, with daptomycin being one of the only last-line therapeutics. Despite this, the daptomycin resistance mechanisms are incompletely understood in clinical, daptomycin-resistant VREfm. The objective of this study was to define the mechanisms associated with daptomycin resistance. To this end, we conducted daptomycin-susceptibility testing and whole-genome sequencing on an unbiased collection of 1000 Australian VREfm clinical isolates. Daptomycin-susceptibility testing showed 18.9% of VREfm were daptomycin-resistant, giving Australia one of the highest rates of resistance globally. A genome-wide association study suggested daptomycin-resistant VREfm contained novel mutations, including within the rifampicin-resistance determining region of rpoB, typically associated with resistance to the front-line antibiotics, rifampicin and rifaximin. Construction of isogenic mutants containing the identified rpoB mutations indicated they conferred cross-resistance to rifampicin and daptomycin. An analysis with international VREfm suggested the novel RpoB mutations were globally distributed, with three co-circulating lineages that have recently emerged and disseminated globally, indicative of ongoing selective pressure. In a murine colonisation model, exposure to rifampicin or rifaximin resulted in the emergence of VREfm that were cross-resistant to rifampicin and daptomycin, indicating exposure to these widely used antibiotics can drive daptomycin resistance in VREfm. Further, patients colonised with VREfm and receiving rifaximin were significantly more likely to harbour rifampicin-resistant, daptomycin-resistant strains than patients not receiving rifaximin. Our study has identified a novel and globally prevalent daptomycin resistance mechanism in VREfm and highlights unanticipated and serious “collateral damage” that may arise in patients following use of rifamycin antibiotics.