The developmental rapidity of nanotechnology poses higher risks of exposure to humans and the environment through manufactured nanomaterials. The multitude of biological interfaces, such as DNA, proteins, membranes, and cell organelles, which come in contact with nanoparticles, is influenced by colloidal and dynamic forces. Consequently, the ensued nano-bio interface depends on dynamic forces, encompasses many cellular absorption mechanisms along with various biocatalytic activities, and biocompatibility that needs to be investigated in detail. Addressing the issue, the study offers a novel green synthesis strategy for antibacterial AgNPs with higher biocompatibility and elucidates the mechanistic in vivo biocompatibility of silver nanoparticles (AgNPs) at the cellular and molecular levels. The analysis ascertained the biosynthesis of G-AgNPs with the size of 25 +/- 10 nm and zeta potential of -29.2 +/- 3.0 mV exhibiting LC50 of 47.2 mu g mL(-1) in embryonic zebrafish. It revealed the mechanism as a consequence of abnormal physiological metabolism in oxidative stress and neutral lipid metabolism due to dose-dependent interaction with proteins such as he1a, sod1, PEX protein family, and tp53 involving amino acids such as arginine, glutamine and leucine leading to improper apoptosis. The research gave a detailed insight into the role of diverse AgNPs-protein interactions with a unique combinatorial approach from first-principles density functional theory and in silico analyses, thus paving a new pathway to comprehending their intrinsic properties and usage.