Objective was to characterize the progression of uterine miocrobiota from calving until establishment of metritis. Uterine swabs were collected at 0 (20 min from calving), 2, 4, 6, and 8 d postpartum (DPP) from 92 cows. Twelve cows were diagnosed with metritis at 4, 6, or 8 DPP (6 ± 2 DPP), and 12 healthy cows were selected for comparison. Swabs (n = 72) collected at 0, 2, and 6 ± 2 DPP were used for metagenomic sequencing of 16S rRNA gene on the Illumina MiSeq platform. A heat map showed that uterine microbiota was established in cows shortly after calving. The microbiota changed rapidly from 0 to 6 ± 2 DPP by decreasing the abundance of Proteobacteria and increasing the abundance of Bacteroidetes and Fusobacteria. At 6 ± 2 DPP, abundance of Bacteroidetes was significantly higher in metritic cows than healthy cows (P < 0.01). Although most genera were shared, healthy and metritic cows could be discriminated based on relative abundance at 0, 2, and 6 ± 2 DPP using discriminant analysis (P < 0.01). Also, discriminant analysis showed that Bacteroides, Filifactor, Porphyromonas, Fusobacterium, and Arcanobacterium/Trueperella were important predictors of metritis. Furthermore, Bacteroides and Fusobacterium were significantly correlated with uterine discharge score (r_s = 0.51 and r_s = 0.49, respectively; P = 0.02). Likewise, at species level, Bacteroides heparinolyticus and Fusobacterium necrophorum were the main bacteria for the development of metritis because they were both prevalent (16.8% and 20.2% in metritic cows; 7.0% and 15.8% in healthy cows) and correlated with uterine discharge score (r_s = 0.42 and r_s = 0.42, respectively; P ≤ 0.05). In addition, there was a second (Fusobacterium gonidiaformans, Helcoccocus ovis, and Filifactor villosus) and third (Bacteroides pyogenes, Porphyromonas levii and others) line of bacteria that acted synergistically with the main bacteria causing metritis.