Thiolate protected metal nanoclusters are emerging materials for the preparation of atomically defined heterogeneous catalysts. Recently it was revealed that the ligands migrated to the support upon cluster deposition, which influences the catalytic behaviour. Here we examined the role of the protecting thiolate ligands on the cyclohexane oxidation for Au38(SR)24 supported on CeO2 and Al2O3. Sulfur containing products were detected. XANES S K-edge measurements revealed SOx species on the support during the reaction. The results indicate (i) an active and complex role of the thiolate ligand and (ii) changes of cluster (surface) structure, depending on support material and reaction conditions.