The effect of spontaneous alloying of non-stoichiometric aqueous Ag–In–S (AIS) and Cu–In–S (CIS) quantum dots (QDs) stabilized by surface glutathione (GSH) complexes was observed spectroscopically due to the phenomenon of band bowing typical for the solid–solution Cu(Ag)–In–S (CAIS) QDs. The alloying was found to occur even at room temperature and can be accelerated by a thermal treatment of colloidal mixtures at around 90 °C with no appreciable differences in the average size observed between alloyed and original individual QDs. An equilibrium between QDs and molecular and clustered metal–GSH complexes, which can serve as “building material” for the new mixed CAIS QDs, during the spontaneous alloying is assumed to be responsible for this behavior of GSH-capped ternary QDs. The alloying effect is expected to be of a general character for different In-based ternary chalcogenides.