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<i>Campylobacter jejuni</i> is the leading cause of foodborne bacterial gastroenteritis in humans worldwide. Contaminated chickens and their products are the main sources of human campylobacteriosis. Therefore, this study aimed to detect the genotypic and virulence genes‘ profiles of multi-drug resistant (MDR) <i>C. jejuni</i> isolates and to assess the effects of sub-inhibitory concentrations (SICs) of eugenol and beta-resorcylic acid on the virulence of avian MDR <i>C. jejuni</i> isolates. These isolates were clustered together with the human isolates via enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) fingerprinting. A total of 345 samples were collected from human stool (100) and different chicken (245) samples in Sharkia Governorate, Egypt. Conventional phenotypic methods identified 113 isolates (32.8%) as <i>C. jejuni,</i> and all <i>C. jejuni</i> isolates were MDR and resistant to erythromycin and ampicillin. The genes <i>vir</i>B11, <i>wla</i>N, and <i>fla</i>A were detected in 52%, 36% and 100% strains, respectively. ERIC-PCR yielded 14 profiles and five main clusters. Interestingly, human and chicken <i>C. jejuni</i> isolates were clustered together in ERIC-PCR clusters II-V, which confirmed the genetic relatedness between the isolates from both origins. Beta-resorcylic acid and eugenol inhibited the invasion of <i>C. jejuni</i> isolates to chicken intestinal cells by 41.66–38.19% and 31.94–29.16%, respectively, and minimized the transcription of <i>fla</i>A, <i>vir</i>B11, and <i>wla</i>N genes in the tested isolates by real-time quantitative reverse transcription PCR (qRT-PCR). In essence, eugenol and beta-resorcylic acid are promising natural antimicrobials for minimizing the virulence of MDR <i>C. jejuni</i> in chickens, thereby managing human campylobacteriosis.