© 2021 The Society for Applied MicrobiologyThe aim of this study is to investigate the phytochemical contents and antibacterial properties of 2-year Prunus avium L. standard cultivars [Cristalina (Cr), 0900 Ziraat (Zr)] and to elucidate the mechanism of action of the extracts on the quorum sensing (QS) system by using homology modelling and molecular docking. Phenolic contents of methanol extract of Cr and Zr stalks were detected by HPLC. As a result, catechin hydrate (6364·67–8127·93 µg g−1) and chlorogenic acid (998·81–1273·4 µg g−1) were found to be the highest in stalk extracts in the two varieties in 2017. All extracts had inhibitory effect on Gram-positive bacteria. Stalk extract of Zr showed higher inhibition rate (86%) on swarming motility. Stalk samples of Zr collected in 2017 and 2018 also reduced biofilm formation by 75 and 73%, respectively. The computational analysis revealed that one of the major component of the extracts, chlorogenic acid, was able to bind to the QS system receptors, LasR, RhlR, and PqsR. Therefore, the mechanism of decreasing the production of virulence factors by the extracts might be through inhibiting these receptors and thus interfering with the QS system.