The present study elucidates the extracellular synthesis of capped silver nanoparticles using processing waste (intestine) of sheep and swine in aqueous media and phosphate buffers incubated with silver nitrate by dispensing with the addition of any capping agent and the advantage of avoiding the agglomeration and loss of nanosized characteristics of AgNPs. The synthesis of Ag-NPs was ascertained by UV-VIS spectrophotometry of the incubated suspension of yellowish-brown at 400-410 nm. The Ag-NPs were further characterized using a High-Resolution Transmission Electron Microscope, which confirmed that the Ag-NPs were primarily spherical and had a size range of 5–100 nm with a maximum frequency fall between 5-20 nm, 21-30 nm, 31-50 nm and a few falls within 51-100 nm. In addition, Ag-NPs synthesized using sheep and pig wastes are characterized by Dynamic Light Scattering, which confirmed the high stability of Ag-NPs with a zeta potential of -27 and -32 mV respectively. Biomolecules and biological extracts of sheep and swine waste act as biogenic reducing and capping agents. Based on the zone of inhibition achieved through the agar well diffusion method, Ag-NPs biosynthesized using sheep waste showed high bactericidal properties against Aeromonas hydrophila, Edwardsiella tarda, and Micrococcus luteus as compared to swine waste-derived AgNPs. The chronic toxicity analysis of biosynthesized Ag-NPs on Pangasianodon hypophthalmus was carried out using stress biomarkers such as an antioxidant enzyme, AChE, and metabolic enzyme activity. Chronic toxicity of synthesized Ag-NPs was found to increase with increased sub-lethal ammonia concentration and temperature. The findings of this study revealed that biosynthesis of capped and non-agglomerated Ag-NPs can be undertaken by using sheep and swine wastes for their potential application in aquaculture based on the properties observed in characterization, bactericidal activity, and physiological responses of the fish.