Single molecules are nanoscale thermodynamic systems with few degrees of freedom. Thus, the knowledge of their entropy can reveal the presence of microscopic electron transfer dynamics, that are difficult to observe otherwise. Here, we apply thermocurrent spectroscopy to directly measure the entropy of a single free radical molecule in a magnetic field. Our results allow us to uncover the presence of a singlet to triplet transition in one of the redox states of the molecule, not detected by conventional charge transport measurements. This highlights the power of thermoelectric measurements which can be used to determine the difference in configurational entropy between the redox states of a nanoscale system involved in conductance without any prior assumptions about its structure or microscopic dynamics.