Selective dehydrogenation of the biomass-derived lignan hydroxymatairesinol (HMR) to oxomatairesinol (oxoMAT) was studied over an Au/Al2O3 catalyst. The reaction was carried out in a semi-batch glass reactor at 343 K under two different gas atmospheres, namely produced through synthetic air or nitrogen. The studied reaction is, in fact, an example of secondary-alcohol oxidation over an Au catalyst. Thus, the investigated reaction mechanism of HMR oxidative dehydrogenation is useful for the fundamental understanding of other secondary-alcohol dehydrogenation over Au surfaces. To investigate the elementary catalytic steps ruling both oxygen-free- and oxygen-assisted dehydrogenation of HMR to oxoMAT, the reactions were mimicked in a vacuum over an Au28 cluster. Adsorption of the involved molecular species—O2, three different HMR diastereomers (namely, one SRR and two RRR forms), and the oxoMAT derivative—were also studied at the DFT level. In particular, the energetic and structural differences between SRR-HMR and RRR-HMR diastereomers on the Au28 cluster were analyzed, following different reaction pathways for the HMR dehydrogenation that occur in presence or absence of oxygen. The corresponding mechanisms explain the higher rates of the experimentally observed oxygen-assisted reaction, mostly depending on the involved HMR diastereomer surface conformations. The role of the support was also elucidated, considering a very simple Au28 charged model that explains the experimentally observed high reactivity of the Au/Al2O3 catalyst.