Ligand exchange is frequently used to introduce new functional groups on the surface of inorganic nanoparticles or clusters while preserving the core size. For one of the smallest clusters, triphenylphosphine (TPP)-stabilized undecagold, there are conflicting reports in the literature regarding whether core size is retained or significant growth occurs during exchange with thiol ligands. During an investigation of these differences in reactivity, two distinct forms of undecagold were isolated. The X-ray structures of the two forms, Au11(PPh3)7Cl3 and [Au11(PPh3)8Cl2]Cl, differ only in the number of TPP ligands bound to the core. Syntheses were developed to produce each of the two forms, and their spectroscopic features correlated with the structures. Ligand exchange on [Au11(PPh3)8Cl2]Cl yields only small clusters, whereas exchange on Au11(PPh3)7Cl3 (or mixtures of the two forms) yields the larger Au25 cluster. The distinctive features in the optical spectra of the two forms made it possible to evaluate which of the cluster forms were used in the previously published papers and clarify the origin of the differences in reactivity that had been reported. The results confirm that reactions of clusters and nanoparticles may be influenced by small variations in the arrangement of ligands and suggest that the role of the ligand shell in stabilizing intermediates during ligand exchange may be essential to preventing particle growth or coalescence.