Avian influenza viruses (AIVs) present an ongoing threat of human infections. Continuous surveillance is important for detecting new infections and verifying prevention and control measures. Swabs of the external environment and throat swabs of employees were collected from six farmers’ markets in Beijing to detect influenza A virus. Positive samples were sequenced, and their genetic characteristics analyzed. In total, 3251 environmental samples were collected from 2019 to 2023, 11 of which were positive for influenza A virus (positivity rate of 0.34%), including nine for H9N2 and two for H7N9. In a genetic analysis, all H7N9 samples showed low pathogenicity, and no mutations at highly pathogenic sites were detected. All 1135 throat swab samples from staff were negative for influenza A virus. At present, the detection rate of AIVs in farmers’ markets is very low, and no adaptive mutations allowing cross-host transmission were found, indicating a low risk of AIV infection among the people of Beijing.