The reduction of the molecular iron-molybdenum-nanocluster, HxPMo12O40⊂H4Mo72Fe30(O2CMe)15O254(H2O)98-y(EtOH)y, was studied using model free isoconversional methods. The reduction kinetics were evaluated using the non-isothermal thermogravimetric measurements at four different heating rates from 5 to 20 °C/min in a 5% hydrogen atmosphere (argon balance). The apparent activation energy dependence on conversion derived from the isoconversional Kissinger–Akahira–Sunose (KAS) and Vyazovkin methods reveals a complex multi-step process with values ranging from 60.8 ± 13.3 to 183 ± 6.3 kJ/mol. The kinetic results were validated by isothermal predictions. The results herein are useful for optimization and development of FeMoC derived Fe–Mo nanoalloy systems.