In this paper, we report a reliable method for transferring hydrophobic, NIR-emitting PbS/CdS core-shell quantum dots (QDs) to water solutions using synthesized in situ dithiocarbamate derivatives of amino acids as stabilizing ligands. Such ligands offer apparent advantages over dihydrolipoic acid (DHLA) derivatives commonly used as ligands stabilizing quantum dots. The most effective phase transfer and the best long-term stability of water dispersions of amino acid-DTC-capped QDs were achieved using lysine dithiocarbamate. In this case, the phase transfer of PbS/CdS nanoparticles from organic to aqueous phase can be completed in 6-8 h. Prepared amino acid-DTC-capped QDs nanoparticles have narrow size distributions, and their hydrodynamic diameter remains below 9 nm. After transferring to water, lysine-DTC-capped PbS/CdS nanoparticles retain their spectroscopic properties for at least 48 h. Moreover, they are not toxic up to concentration corresponding to about 7 μg/cm3 of PbS/CdS, which is sufficient for their application in biological systems. In addition, lysine-DTC-capped PbS/CdS QDs can be straightforwardly modified by layer-by-layer polyelectrolyte coating.