The increasing emergence and spread of antibiotic resistance accelerate the desire for antibiotic alternatives. Plant extracts have emerged as a promising and relatively unexplored area of research as potential substitutes. Herein, we investigated the prevalence and distribution patterns of bacteria on egg surfaces and evaluated the inhibitory effects of mangosteen extract on these surface bacteria. In addition, we examined the antioxidant activity and egg quality in improving the ability of mangosteen extract. The results showed that the predominant bacteria isolated from eggshells were Gram-positive, with and as the dominant genera. Notably, mangosteen extract exhibited significant bactericidal activity, effectively inhibiting Gram-positive bacteria on the surface of chicken eggshells. Moreover, the supplementation of mangosteen extract in the feed of laying hens yielded a noteworthy improvement in egg quality, accompanied by positively shaped structure and function of microbial communities on the egg surface and in the feces. Collectively, our findings suggested that mangosteen extract was an effective alternative to traditional antibiotics, offering valuable insights for animal husbandry development.