The synthesis, crystal structure, and magnetic properties of [Mo-3(CoCO)Se-4(dmpe)(3)Cl-3] (1), [Mo-3(CoCl)Se-4(dmpe)(3)C-3] (2), and [Mo-3(CoCl)Se-4(dmpe)(3)Cl-3](TCNQ) ([2](TCNQ)) (dmpe = 1,2-bis(dimethylphosphanyl)ethane; TCNQ = 7,7,8,8-tetracyanoquinomethane) cubane-type complexes with 16, 15, and 14 metal electrons, respectively, are reported. These compounds complete the series of cobalt-containing Mo(3)CoQ(4) (Q = S, Se) cubane-type complexes, which allows a complete analysis of the consequences of replacing the inner chalcogen and the metal electron count on the structural, magnetic, and electrochemical properties. The experimental evidence is theoretically supported and rationalized on the basis of density-functional theory calculations. For the 15-metal electron [Mo-3(COCl)Se-4(dmpe)(3)Cl-3] complex with S = 1/2, both electron paramagnetic resonance and theoretical studies give support to a spin density mainly located on the heteroatom. The nature of the highest occupied molecular orbital upon chalcogen exchange within the Mo(3)CoQ(4) (Q = S, Se) series remains essentially unchanged, whereas the nature of the ligand attached to Cc (Cl or CO) results in a different ordering of the molecular orbital scheme. This behavior is explained by the absence of backdonation between an occupied d orbital of Co to an empty pi* Cl orbital, to yield frontier orbitals that differ from those of previous models.