Objective To investigate the microbial contamination situation of health foods sold in Beijing, and provide a scientific basis for quality assurance of health foods. Methods 4 325 samples of health foods sold in Beijing from 2011 to 2019 were tested for the contamination of aerobic plate count, moulds and yeasts, coliforms and pathogenic bacteria according to the method specified in GB 4789. Results In the 9 years, the total qualification rate was 98.71%(4 269/4 325), and the qualification rate increased from 94.52%(207/219) in 2011 to 99.54%(653/656) in 2019 year by year. There was a statistically significant difference in the different dosage form of health foods(χ²=34.94,P<0.01), the qualification rate of paste sample was the highest(100.00%,50/50),and that of the following dosage forms decreased in order:oral liquid (99.80%,510/511), tablets (99.21%,1 135/1 144), solid granules (99.13%,340/343), capsules (98.63%,1 803/1 828), pills (97.06%,66/68), and health tea (95.80%,365/381). The result of four microbial indicators of 4 325 health foods showed that aerobic plate count was the highest, followed by moulds and yeasts, and coliforms, which were 0.83%(36/4 325), 0.46%(20/4 325) and 0.30%(13/4 325) respectively. There was no Salmonella and Staphylococcus aureus detected in all samples. However, among the 156 samples, 185 strains were isolated which contained a variety of common environmental bacteria and conditional pathogens. Conclusion The microbiological qualification rate of health food sold in Beijing increased year by year from 2011 to 2019, but there was still a certain risk of microbial contamination.