The objective was to evaluate the shift in uterine microbiota after treating cows with metritis with chitosan microparticles (CM). A subset of cows (n = 89) were randomly sampled from a larger study (n = 826) where cows had been randomly assigned to 1 of 3 treatments: CM = intrauterine infusion of 24 g of CM dissolved in 40 mL of sterile distilled water at the time of diagnosis (D0), D2 and D4; Ceftiofur = subcutaneous injection of 6.6 mg/kg of ceftiofur crystalline-free acid (Excede, Zoetis) in the base of the ear at D0 and D3; Control = no intrauterine or subcutaneous treatment. A group of healthy (HTH) cows matched by days in milk at metritis diagnosis was added for comparison. Uterine swabs were collected from CM (n = 21), CEF (n = 25), CON (n = 23), and HTH (n = 20) on D0, D3, D6, D9, and D12. Swabs were used for genomic DNA extraction and sequencing of the V4 hypervariable region of the 16S rRNA gene on the Illumina MiSeq platform. Principal coordinate analysis paired with permutation ANOVA at the phylum and genus level showed that the uterine microbiome was similar among all metritic groups on D0, but different (P ≤ 0.001) from HTH cows. Additionally, the microbiome of CEF cows shifted more rapidly toward HTH cows, with CM cows being the slowest to shift toward HTH and CON being intermediate. Comparison of relative abundance at the phylum level showed that metritic cows had greater (P ≤ 0.05) abundance of Bacteroidetes and Fusobacteria, and lesser abundance of Proteobacteria and Tenericutes on D0 than HTH cows. CM tended (P ≤ 0.10) to have a greater overall abundance of Bacteroidetes compared with CEF, and greater abundance of Fusobacteria on D3 compared with CEF and CON. In summary, CM slowed the progression toward a healthy uterine microbiome, whereas CEF hastened the progression toward a healthy uterine microbiome.