Bacterial infection of the uterus affects a high proportion of dairy cows during the postpartum period. Failure to clear within three weeks after calving is defined as postpartum endometritis. The economic impact of endometritis in Ireland has been estimated to be in the range of €76 to €284 million per year. We hypothesized that endometritis is the result of the interplay of microbiome and immune status of the cow. We previously showed that the endometrial transcriptome is remodeled from a proinflammatory stage to a proliferative and repair stage within three weeks postpartum and that this transition is arrested in cows suffering endometritis. This work showed that the composition of the microbiome in the reproductive tract is associated to the postpartum health status of dairy cows. Differences between endometritic and healthy animals are not related to the presence/absence of specific pathogens but rather to a community shift with an important reduction of bacterial diversity. Our data suggests that parturition conveys the mixing of vaginal and uterine microbiomes, which subsequently are differentiated. This microbial succession is likely associated to early clearance in the healthy cow. In contrast, a delayed succession was observed in cows developing endometritis. The endometritis-associated changes in the microbial community occurring as early as 7 days postpartum can be the basis of an early detection test of bovine postpartum endometritis.