In many temperate breeding birds, earlier breeders have higher seasonal reproductive success, but it is unclear what prevents all individuals from breeding earlier. Early breeders face variable environmental conditions, and the ability to shift phenotype to match these conditions may constrain breeding time. Microbial diversity is of known importance to host health and may influence the host’s ability to adjust phenotype. Gut microbiota can also mediate adaptive changes in body mass, in addition to being influenced by diet. In this study, we tested whether cloacal microbiome diversity, or within-individual changes in microbial diversity, differ in earlier and later breeding female tree swallows (Tachycineta bicolor). Earlier breeders, which were heavier at first capture, had more diverse microbiomes. Birds that laid earlier lost more mass and decreased more in microbial diversity from mid incubation through early provisioning. In contrast, clutch initiation date did not predict mass change or diversity gain between early and later provisioning. Our results demonstrate that both microbial diversity and the flexibility of diversity differ by timing of breeding, and thus may serve as physiological indicators of individual quality. These results are consistent with the idea that microbial flexibility may affect an individual’s ability to shift phenotype including body mass changes from incubation to provisioning, and therefore, could impact individual fitness and timing of breeding.