Molybdenum(VI) catalysts were obtained from methanol or acetonitrile by the reaction of [MoO2(C5H7O2)2] and isonicotinoyl- or nicotinoyl-based aroylhydrazones. Reactions in methanol resulted in the formation of the mononuclear complexes [MoO2(L1–4)(MeOH)] (1a–4a), while the ones in acetonitrile provided polynuclear complexes [MoO2(L1–4)]n (1–4). Crystals of polynuclear compound, [MoO2(L3)]n∙H2O (3∙H2O), suitable for X-ray diffraction analysis were obtained by the solvothermal procedure at 110 °C. Complexes were characterized by infrared spectroscopy (IR-ATR), nuclear magnetic resonance (NMR), elemental analysis (EA), and thermogravimetric analysis (TGA). The prepared catalysts were tested in alcohol oxidation reactions. Carveol, cyclohexanol, and butan-2-ol were investigated substrates. Because the alcohol oxidations are very challenging due to various possible pathways, the idea was to test different oxidants, H2O2, TBHP in water and decane, to optimize the researched catalytic system.