The present study examines the stability and cytotoxicity of two quantum dots (QDs) systems in cell culture medium in the presence and absence of a thin layer of a ZnS shell. The two systems were built from a core, CdSe, and surface modified with glutathione (GSH), named CdSe∼GSH and CdSe/ZnS∼GSH. CdSe/ZnS∼GSH QDs exhibited a high photostability with a pronounced enhancement in photoluminescence in cell culture medium. Both systems showed insignificant reduction in cell viability of HFB-4 and MCF-7 cell lines in the dark. Following 60 min of low laser power exposure (irradiance of 10 mW cm−2), CdSe∼GSH QDs showed a remarkable decrease in cell viability, which may result from the detachment of GSH molecules, whereas CdSe/ZnS∼GSH QDs showed an insignificant decrease either immediately after irradiation or even 2 h post-exposure, which can be attributed to the high affinity between ZnS and GSH coatings. This study demonstrated that a thin layer of ZnS shell played a crucial role in the stability of CdSe/ZnS∼GSH QDs in cell culture medium with an improvement in luminescence efficiency, whereas surface modification with GSH molecules in the presence of ZnS showed no significant cytotoxic effects before or after photoirradiation, which makes this system attractive for several biomedical applications.