To estimate the relative fitness differences between glycopeptide-resistant Enterococcus faecium (GREF) and glycopeptide-susceptible E. faecium (GSEF) from yearly surveillance data on the occurrence of GREF in Danish poultry farm environments. A population genetic model was adapted to retrospectively estimate the biological fitness cost of acquired resistance. Maximization of a likelihood function was used to predict the longitudinal persistence of acquired resistance. Our analysis suggests strong selection against GREF following the 1995 ban on the glycopeptide growth promoter avoparcin. However, parameterizing the model with two selection coefficients suggesting a reduced negative effect of the acquired resistance on bacterial fitness over time significantly improved the fit of the model. Our analyses suggest that the acquired glycopeptide resistance will persist for >25 years. Conclusions Acquired resistance determinants in commensal E. faecium populations in Danish farm environments are likely to persist for decades, even in the absence of glycopeptide use.