The ability of gold(I) thiolates to self-assemble into supramolecular architectures opens the route for a new class of nanomaterials with a unique structure–optical property relationship. However, for a confirmed structure–optical property relationship, a control of the supramolecular architectures is required. In this work, we report a simple synthesis of sub-100 nanometer gold–cysteine and silver doped gold–cysteine supramolecular assemblies. We explore in particular silver-doping as a strategy to enhance the optical properties of these supramolecular assemblies. By an accurate characterization of as-synthesized supramolecular nanoparticles, we have been able to measure for the first time, their absolute two-photon absorption cross-section, two-photon excited fluorescence cross-section and first hyperpolarizabilities at different near-IR wavelengths. Huge values are obtained for silver doped gold–cysteine supramolecular assemblies, as compared to their corresponding undoped counterpart. In addition, we employ DFT and TD-DFT methods to study the geometric and electronic structures of model gold–cysteine and silver doped gold–cysteine compounds in order to address the structure−linear/nonlinear optical property relationship. The aim is to gain insights into the origin of the nonlinear optical enhancement of silver-doped gold supramolecular assemblies.