Visible light emitting ZnO quantum dots (QDs) were synthesized by a modified sol–gel method and in situ coated with the amino acid cysteine to modify their surface chemistry and govern the crystal growth process. Surface chelation by a hydrophilic thiol such as cysteine offered a fine control over the particle size and modulated the optical emission and its stability by reducing the density of surfacial oxygen deficiencies and also induced the formation of hierarchical nanostructures in the solution. TEM and XRD results confirmed the formation of mono-dispersed and spherical ZnO QDs in the size range 2.5–3.8 nm. The modulation of band gap energies was manifested in the visible emission of cysteine modified QDs, which was found to be remarkably stable for cell labeling applications, when compared to the photoluminescence of conventional ZnO QDs.