In this paper, an aqueous-based route has been developed to prepare highly luminescent glutathione (GSH)-capped Mn-doped ZnS quantum dots (QDs). The dots obtained have an average diameter of 4.3 nm and exhibit the Mn2+-related orange luminescence with very low surface defect density. The highest photoluminescence was observed for a Mn2+ to Zn2+ molar ratio of 3%. Consecutive overcoating of the Mn:ZnS@GSH QDs by a ZnS shell was done, and the core/shell structured QDs exhibit a PL quantum yield of 23%. Transmission electron microscopy, X-ray powder diffraction, electron spin resonance, X-ray photoelectron spectroscopy, UV-visible spectroscopy and spectrofluorometry have been used to characterize the crystal structure, the doping status, and the optical properties of the doped-QDs. Our systematic investigation shows that Mn:ZnS/ZnS@GSH QDs are highly promising fluorescent labels in biological applications.