Different from negatively charged CuInS2 (CIS) based quantum dots (QDs), positively charged QDs are difficult to obtain in good optical quality, but are desirable for certain applications. We herein present a general synthesis strategy that allows for a universal surface modification of ternary CIS based QDs with thiol containing ligands. The idea behind the synthesis design is, to apply a ZnS shell first for passivating and protecting the core QDs, and then add a second ZnS shell for the functionalization via ligand exchange. Whereby easy ligand exchange with thiolated molecules is systematically set up, by using a weak bonding amine ligand for the second shell. Molecules with various terminal groups were used to functionalize the nanoparticles and stabilize them in different media making any surface charge and polarity accessible. Surface defect chemistry seemed to play an important role in our synthesis strategy, therefore to gain a deeper understanding how these defect sites can alter the electronic structure of core/shell nanoparticles theoretical calculations based on density functional theory were performed, whilst structural, colloidal and optical properties were characterized experimentally (by dynamic light scattering, x-ray diffraction, infrared spectroscopy, zeta potential, absorption- and (time resolved) photoluminescence measurements).