Recently, nanotechnology has become an important research field involved in the improvement of animals' productivity, including aquaculture. In this field, silver nanoparticles (AgNPs) have gained interest as antibacterial, antiviral, and antifungal agents. On the other hand, their extensive use in other fields increased natural water pollution causing hazardous effects on aquatic organisms. Quercetin is a natural polyphenolic compound of many plants and vegetables, and it acts as a potent antioxidant and therapeutic agent in biological systems. The current study investigated the potential mitigative effect of quercetin nanoparticles (QNPs) against AgNPs-induced toxicity in Nile tilapia via investigating liver function markers, hepatic antioxidant status, apoptosis, and bioaccumulation of silver residues in hepatic tissue in addition to the whole-body chemical composition, hormonal assay, intestinal enzymes activity, and gut microbiota. Fish were grouped into: control fish, fish exposed to 1.98 mg L-1 AgNPs, fish that received 400 mg L-1 QNPs, and fish that received QNPs and AgNPs at the same concentrations. All groups were exposed for 60 days. The moisture and ash contents of the AgNP group were significantly higher than those of the other groups. In contrast, the crude lipid and protein decreased in the whole body. AgNPs significantly increased serum levels of ALT, AST, total cholesterol, and triglycerides and decreased glycogen and growth hormone (*** p < 0.001). The liver and intestinal enzymes' activities were significantly inhibited (*** p < 0.001), while the oxidative damage liver enzymes, intestinal bacterial and Aeromonas counts, and Ag residues in the liver were significantly increased (*** p < 0.001, and * p < 0.05). AgNPs also significantly upregulated the expression of hepatic Hsp70, caspase3, and p53 genes (* p < 0.05). These findings indicate the oxidative and hepatotoxic effects of AgNPs. QNPs enhanced and restored physiological parameters and health status under normal conditions and after exposure to AgNPs.