For the interpretation of clinical findings of endometritis and the development of disease prevention and intervention strategies a better understanding of the dynamics and interactions within intrauterine bacterial communities in healthy and diseased cows is required. To gain deeper insights into fluctuations within the uterine microbiota, intrauterine samples were collected from 122 cows at the day of calving, days 3, 9, 15, 21 and 28 postpartum. A total of 2052 bacterial isolates were identified by Fourier-transform-infrared spectroscopy. This culturomics-based approach showed that the aerobic uterine microflora comprised a huge diversity of bacteria belonging to 202 different species, representing 76 genera, with members of the genus Staphylococcus (24.2%) being predominant. On species level the uterine microflora was dominated by Trueperella pyogenes (13.2%), Escherichia coli (11.2%), Staphylococcus xylosus (5.4%), Bacillus pumilus (5.2%) and Streptococcus uberis (4.9%). Comparative analysis of uterine bacteria from cows with different vaginal discharge scores (VDS) revealed health status specific temporal microbial diversifications. Although the intrauterine flora of all VDS groups was dominated by T. pyogenes, E. coli and Staphylococcus spp., the relative number of bacteria differed between VDS groups. The presence of T. pyogenes on days 15 and 21 significantly increased the risk of VDS 2 and 3 at day 21, whereas Staphylococci at day 9 reduced the likelihood of VDS 3 (P<0.05). This study demonstrates that intrauterine bacterial infections are highly dynamic processes and that bacterial species follow specific patterns of progression, which require further research to decipher their potential role in uterine disease development.