Developing the chemistry of octahedral chalcogenide molybdenum and tungsten cluster complexes in the context of applications in biology and medicine, in this work a series of water-soluble neutral cluster complexes [{M6Q8}(P(C2H4CONH2)3)6] (M = Mo, W; Q = S, Se) have been obtained by simultaneous replacement of inner and terminal halide ligands in [{M6I8}I6]2− with chalcogenide and organic phosphine ligands and characterized by single-crystal X-ray diffraction analysis, 1H and 31P NMR spectroscopies, elemental analysis, and UV–vis spectroscopy. The amide groups of the organic ligands, on the one hand, contribute to the solubility of the resulting clusters in water and, on the other hand, are able to form an extensive network of hydrogen bonds, leading to the crystallization of the complexes from aqueous solutions. Despite this fact, the complexes have sufficient solubility and stability in aqueous solutions, which made it possible to demonstrate their low cytotoxicity on Hep-2 cells (IC50 were not reached even at concentration up to 4 mM). The resulting clusters are among the most biocompatible of the octahedral clusters studied to date and are the starting point for the development of a new family of X-ray contrast agents.