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Determining whether endometrial microbial isolates are pathogens, contaminants, or even part of the “normal” microbiome is extremely complex, particularly given the absence of “gold standard” tests for endometritis. Population-level benchmarking and temporal monitoring can provide novel insights and a wider context to improve understanding. This study aimed to (i) estimate the prevalence of endometrial isolates from swabs of Thoroughbred broodmares in Newmarket, UK between 2014 and 2020; and (ii) evaluate the effects of year, mare age, and cytology findings on isolate prevalence. Generalised linear mixed models with a logit link, both null models and models using year of sampling, mare age, or cytology findings as predictors, were fitted to estimate isolate prevalence. Over the 7-year period, data were available from 18,996 endometrial-swab samples from 6050 mares on 290 premises. The overall isolate prevalence was 35.5% (95% confidence interval (CI) 33.0–37.9), and this varied significantly between years. The most prevalent isolates were β-hemolytic <i>Streptococcus</i> (17.9; 95% CI: 17–19) and <i>E. coli</i> (10.3%; 95% CI: 9.0–11.6). Isolate prevalence increased with mare age except for <i>E. coli</i> isolates, and with increasing category of cytology findings except for α-hemolytic <i>Streptococcus</i> isolates. The results provide novel estimates of isolate prevalence and highlight knowledge gaps around potential complexities in the interpretation of findings.