The composition and structure of inorganic shells grown over CdSe semiconductor nanocrystal dots and rods were optimized to yield enhanced photoluminescence properties after ligand exchange followed by coating with phytochelatin-related peptides. We show that, in addition to the peptides imparting superior colloidal properties and providing biofunctionality in a single-step reaction, the improved shells and pretreatment with UV irradiation resulted in high quantum yields for the nanocrystals in water. Moreover, peptide coating caused a noticeable red-shift in the absorption and emission spectra for one of the tested shells, suggesting that exciton-molecular orbital (X-MO) coupling might take place in these hybrid inorganic-organic composite materials.