A unique series of unsymmetrically substituted [Mo3S4(dmpe)3Cl3–x(dca)x]PF6 (x = 0–3) clusters that feature mixed Cl/dca terminal ligands, prepared by thermal reaction of [Mo3S4(dmpe)3Cl3]PF6 (PF6) [dmpe = 1,2-bis(dimethylphosphanyl)ethane] with sodium dicyanamide [Na(dca); dca = dicyanamide] is reported. The cluster/Na(dca) ratio, reaction time as well as the nature of the solvent dictate the relative ratio of [Mo3S4(dmpe)3Cl2(dca)]PF6 (PF6), [Mo3S4(dmpe)3Cl(dca)2]PF6 (PF6) and [Mo3S4(dmpe)3(dca)3]PF6 (PF6). An electrospray ionization mass spectrometry (ESI-MS) based protocol was employed for high-throughput optimization of reaction conditions directed to obtain [2–4]PF6 in optimal yield. The incorporation of dca confers significant polarity differences on the [2–4]PF6 series, so that compounds [2–4]PF6 can be efficiently isolated in analytically pure form after silica gel chromatography and represent the first examples of unsymmetrically substituted Mo3S44+ clusters that feature mixed terminal ligands. The structural, spectroscopic and electrochemical consequences of the stepwise Cl/dca replacement along the [1–4]PF6 series are also presented. The distinctive UV/Vis and electrochemical features along the [1–4]PF6 series illustrate the ability to fine-tune the physicochemical properties of Mo3S44+ clusters upon stepwise dca incorporation more efficiently than upon complete ligand substitution.