This study describes the synthesis of novel biological hybrid materials, where 3D structures were obtained using gold nanoparticles (AuNps) and methionine (Met) in a one-step procedure in aqueous media. The type of nanostructure can be controlled by tuning the intermolecular interactions between Met and AuNp, which strongly depends on the pH used for the synthesis. Computational simulation using the density-functional theory (DFT) showed that the AuNp–Met 3D structures are formed upon reorientation of Met molecules so that the backbone amine groups interact via H-bonds. These findings were experimentally confirmed using FTIR and UV–vis spectroscopy.