Objective To understand the status of microbial contamination in commercially prepared beverages sold in Huzhou City, and to provide reference data for health supervision and the improvement of standards for commercially prepared beverages in China. Methods In 2023, a total of 220 samples of freshly prepared beverages were collected in batches from hotels, restaurants, beverage shops, and other food and beverage service establishments in Huzhou City. All samples were tested for four hygiene indicator microorganisms (total bacterial count, mold, yeast, and Escherichia coli) and three foodborne pathogenic bacteria (Staphylococcus aureus, Salmonella, and Listeria monocytogenes) according to relevant national standards. Results The overall non-conformity rate for the 220 samples of freshly prepared beverages monitored in this study was 19.09%. Specifically, the non-conformity rate for total bacterial count was 5.00%, and that for E. coli was 17.73%. Among the foodborne pathogenic bacteria, S. aureus was detected in 1.82% of the samples, with all counts <104 CFU/mL.There was a statistically significant difference in the non-conformity rate for total bacterial count among different types of freshly prepared beverages (χ2=27.915, P<0.05). In ]terms of geographical location, the non-conformity rates for total bacterial count and E. coli in freshly prepared beverages collected from rural areas were much higher than those from urban areas, with statistically significant differences (Fisher's χ2 bacteria=11.327, P<0.05; Fisher's χ2Escherichia coli= 19.853, P<0.05). Mold and yeast were detected in all types of freshly prepared beverages, with the maximum detected value for mold being 4.06 lg CFU/g and that for yeast being 5.37 lg CFU/g. Conclusion The contamination of hygiene indicator microorganisms in freshly prepared beverages in Huzhou City is a matter of concern, primarily due to the high rates of exceeding the limits for E. coli and total bacterial count. Mold and yeast were also detected, with a relatively high average count of yeast.It is recommended that the country establish and improve the limit standards for microorganisms such as mold and yeast in freshly prepared beverages as soon as possible, in order to more effectively address the increasingly complex hygiene monitoring and supervision of freshly prepared beverages.