The gut, urine, and vaginal microbiomes play significant roles in the pathogenesis of recurrent urinary tract infections (rUTIs). Analysis of these microbiota has shown distinct associations with urinary tract infections. Encouraging data indicate that rUTIs may be responsive to microbiome treatments such as fecal microbiota transplantation (FMT) expanding potential treatments beyond antibiotics, hydration and behavioral interventions. If successful, these non-antibiotic therapies have potential to increase time between rUTI episodes as well as reduce the prevalence of multidrug-resistant organisms (MDROs). In this review, we discuss the role of the three microbiomes in the pathogenesis of rUTI and utilization of live biotherapeutic products as therapy for rUTI.