For biological and medical applications, a definable nanomaterial and knowledge on its fate after administration are highly recommended if not mandatory. Here, we synthesized a water-soluble gold nanocluster by sodium borohydride reduction of chloroauric acid in the presence of 5,5′-dithio-bis(2-nitrobenzoic acid). The resulting gold nanocluster displayed the physical characteristics of a cluster containing an inner core of about 100 gold atoms that was surrounded by an organic monolayer made of about 30 thioaminobenzoic acids (TAB) and 14 anionic thionitrobenzoic acids (TNB). The mixed TAB-,TNB-protected gold nanocluster reacted well in water with thiolated peptides containing a nuclear localization signal (NLS) or a nuclear export signal (NES) mainly by exchange of the TNB, providing gold nanoclusters equipped with 8–9 intracellular active peptides and a remaining ligand coverage consisting mostly of the zwitterion TAB. The behavior of these peptide–gold nanoclusters inside the cytosol and nucleus of cells was then assayed using an electroporation procedure allowing transient plasma membrane permeability. Light and electron microscopy observations demonstrated a consistent inflow and diffusion of the gold nanoclusters into the cytosol. Inside the living cells, the distribution of the gold nanoparticles was specifically driven by the appended signal peptides in a manner similar to the distribution of NLS and NES-bearing proteins, demonstrating diffusion ability, stability, and usage of these definable ligand-substituted gold nanoclusters for intracellular applications.