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Background The emergence of drug-resistant phytopathogenic bacteria and the need for new type of biological disease-control agents have accelerated efforts toward searching for alternative candidates with a low propensity for resistance development. In this study, a new series of stilbene-based peptoid mimics were synthesized, and their biological activities were evaluated against citrus pathogenic bacteria in vitro and in vivo. Results Antibacterial bioassay results showed that the dicationic peptoid mimics 9a and 9b displayed excellent bioactivity against Xanthomonas axonopodis pv citri, with the minimum inhibitory concentration (MIC) values of 25 μM, which were superior to those of commercial copper biocides Delite (200 μM) and Kasumin Bordeaux (100 μM). In vivo bioassay further confirmed their control efficacy against plant bacterial diseases. In addition, the antibacterial mechanism of action elucidated their membrane-disruption effects resulting in the leakage of the bacterial membranes, which was similar to that of antimicrobial peptides (AMPs). Moreover, the inhibition effect on biofilm formation of peptoid mimics has also been demonstrated. Conclusion Stilbene-based peptoid mimics synthesized in this study showed promising antibacterial activity with a potent membrane-disruptive mechanism. The results suggested that stilbene-based peptoid mimics have the potential as a new type of bactericide candidates for citrus disease protection. This article is protected by copyright. All rights reserved.