Animals host microbial communities (‘microbiomes’) that inhabit most every niche of their body and these microbiomes can influence host development, physiology, and behavior. Previous work has predominantly focused on the gut, oral, and skin microbiomes, leaving open the question of how other microbiomes, such as the reproductive microbiome, are related to host phenotype and, most importantly, host fitness. Here, we assessed how multiple aspects of the cloacal microbiome are related to various fitness-related traits in free-living female tree swallows (Tachycineta bicolor), a commonly studied cavity-nesting bird. Cloacal swabs were collected from female tree swallows during incubation from 2017 to 2019, and 16S rRNA gene amplicon sequencing was used to characterize cloacal microbiomes. We considered the following fitness-related traits: lay date, number of eggs laid, average brood mass, number of young fledged, hematocrit, and H:L ratios. Given the growing trend of measuring various microbiomes in a diversity of contexts, our results may underscore the importance of determining rather than assuming the functional significance of microbiomes in free-living animals.