The phosphine-stabilized gold cluster [Au-6(Ph2P-o-tolyl)(6)](NO3)(2) is converted into an active nanocatalyst for the oxidation of benzyl alcohol through low-temperature peroxide-assisted removal of the phosphines, avoiding the high-temperature calcination process. The process was monitored using in situ X-ray absorption spectroscopy, which revealed that after a certain period of the reaction with tertiary butyl hydrogen peroxide, the phosphine ligands are removed to form nanoparticles of gold which matches with the induction period seen in the catalytic reaction. Density functional theory calculations show that the energies required to remove the ligands from the [Au6Ln](2+) increase significantly with successive removal steps, suggesting that the process does not occur at once but sequentially. The calculations also reveal that ligand removal is accompanied by dramatic rearrangements in the topology of the cluster core.