The current investigation aims to study the bio route preparation of chitosan capped-silver nanoparticles using aqueous flower extract of the Achillea ptarmica plant. The biosynthesized silver nanoparticles/chitosan (Ag NPs@CHI) were characterized by various spectroscopic techniques. The creation of Ag nanoparticles over the chitosan was initially determined by the presence of a single broad peak at 545 nm that was recorded by the UV–Vis spectrum. The presence of poly-dispersity, spherical shape and nanosizes in the Ag NPs@CHI were verified by the TEM and SEM pictures. The purity and crystalline nature of the prepared Ag NPs@CHI were confirmed by XRD analysis. In vivo, Ag NPs@CHI decreased the inflammatory cells presence in the colon and ileum, lowered the levels of IL-17A, IL-1β, IL-6, and TNF-α, raised the levels of IL-10 and IL-4 in colon tissues, enhanced acetate and propionate production. The findings revealed that Ag NPs@CHI have the potential to boost intestinal structure restoration, decrease levels of inflammatory cytokines and enhance short-chain fatty acid (SCFA) levels. Our research demonstrated that Ag NPs@CHI can safeguard the intestinal barrier by upregulating the expression of Claudin-1 and Occludin. Furthermore, silver nanoparticles suppressed the MAPK signaling pathway to ameliorate the inflammatory condition. Following the completion of clinical trials, these novel nanoparticles could serve as a promising new treatment for diarrhea in humans.