The developmental rapidity of nanotechnology poses the higher risks of exposure to humans and the environment through manufactured nanomaterials. The multitude of biological interfaces, like DNA, proteins, membranes, and cell organelles, which come into contact with nanoparticles, are influenced by colloidal and dynamic force. Consequently, the ensued nano-bio interface depending on the dynamic forces, encompass many cellular absorption mechanisms along with various biocatalytic activities, and biocompatibility that needs to be investigated in detail. Addressing to 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 level. The analysis ascertained the biosynthesis of G-AgNPs with size of 25 ±10 nm and zeta potential of -29.2 ± 3.0 mV exhibiting LC50 of 47.2 g/mL in embryonic zebrafish. It revealed the mechanism as a consequence of abnormal physiological metabolisms in oxidative stress and neutral lipid metabolism due to dose-dependent interaction with proteins like he1a, sod1, PEX protein family, and tp53 involving amino acids like 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 comprehend their intrinsic properties and usage.