The key steps for seed mediated growth of noble metal nanoparticles involve primary and secondary nucleation, which depends upon the energy barrier and ligand supersaturation standards of the medium. Herein we report the unique case of methionine (Met) controlled growth reaction, which rather proceeds via impeding secondary nucleation in presence of citrate stabilized gold nanoparticle (AuNP). The interaction between freshly generated Au+ and thioether group of Met in the medium restricts the secondary nucleation process involving further Au+ reduction. This incomplete conversion of Au+ results in a significant enhancement of the zeta (ζ) potential even at low concentration of Met. Furthermore, the aurophilic interaction of Au+ controls the self-assembly process of the in situ generated emissive nucleated particles. Nucleation of primary particles on seed surface, their segregation and time dependent conversion to larger particles within self-assembly confirm the nonclassical growth, which has further been explored with Met containing bio-inspired peptides.