Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infection in infants. It is being increasingly recognised as a cause of morbidity and mortality in the elderly. Microbial dysbiosis in the respiratory tract has been hypothesized to predispose individuals to severe RSV infection. This study explores changes in the bacterial community over the course of a controlled human challenge study. From 37 healthy adult patients exposed to a challenge inoculum of RSV, throat swabs were collected daily for 10 days during quarantine and on days 14 and 28 post quarantine. Swabs were processed for bacterial and viral quantification and 16S rRNA gene sequencing. Over the course of the study three clinical outcomes were observed; clinical cold (n = 17), asymptomatic infection (n = 6) or no infection (n = 14). These three outcome groups had no significant differences in the bacterial load, diversity or community composition at baseline. Over the twenty-eight days following RSV inoculation no significant changes in the bacterial community were observed between the outcome groups. This study of healthy adults revealed no major changes in the bacterial community of the respiratory tracts following RSV inoculation, suggesting that this microbial community is resilient to viral perturbations.