Syntheses of metal sulfide nanocrystals (NCs) by heat-up routes in the presence of thiols yield NC arrangements difficult to further functionalize and transfer to aqueous media. By means of different NMR techniques, and exemplified by Ag2S NCs, a metal-organic polymer formed during the synthesis acting as a ligand has been identified to be responsible for such aggregation. In this work, a new synthetic hot-injection strategy is presented to synthesize Ag2S NCs which are easily ligand exchangeable in water. Furthermore, the hot-injection route allows an extra NC treatment with Se to produce Ag2S/Ag2(S,Se) NCs with improved optical properties with respect to the Ag2S cores, and better resistance to oxidation, as demonstrated by X-ray absorption experiments.