The electronic relaxation dynamics of gold monolayer protected clusters (MPCs) are influenced by the hydrocarbon structure of thiolate protecting ligands. Here, we present ligand-dependent electronic relaxation for a series of Au25(SR)18- (SR = SC8H9, SC6H13, SC12H25) MPCs using femtosecond time-resolved transient absorption spectroscopy. Relaxation pathways included a ligand-independent femtosecond internal conversion and a competing ligand-dependent picosecond intersystem crossing process. Intersystem crossing was accelerated for the aliphatic (SC6H13, SC12H25) thiolate MPCs compared to the aromatic (SC8H9) thiolate MPCs. Additionally, a 1.2 THz quadrupolar acoustic mode and a 2.4 THz breathing acoustic mode was identified in each cluster, which indicated that differences in ligand structure did not result in significant structural changes to the metal core of the MPCs. Considering that the difference in relaxation rates did not result from ligand-induced core deformation, the accelerated intersystem crossing was attributed to greater electron-vibrational coupling to Au-S vibrational modes. The results suggested that the organometallic semiring was less rigid for the aliphatic thiolate MPCs due to reduced steric effects, and in turn, increases in nonradiative decay rates were observed. Overall, these results imply that the protecting ligand structure can be used to modify carrier relaxation in MPCs.