The ligand exchange reaction between heteroatom doped (Pd, Pt) Au25(2-PET)18 (2-PET = 2-phenylethylthiolate) clusters and enantiopure 1,1′-binaphthyl-2,2′-dithiol (BINAS) was monitored in situ using chiral high-performance liquid chromatography (HPLC). During the ligand exchange reactions, replacement of two protecting thiols (2-PET) with one new entering BINAS ligand on the cluster surface occurs. The rigid dithiol BINAS adsorbs in a specific mode that bridges the apex and one core site of two adjacent S(R)–Au–S(R)–Au–S(R) units. This is the most favorable binding mode and theoretically preserves the original structure. A kinetic investigation on these in situ ligand exchange reactions revealed a decrease in reactivity after multiple exchange. A comparison of relative rate constants demonstrates a similar exchange rate toward BINAS for both (Pd, Pt) systems. The possible structural deformation after incorporation of BINAS was investigated by X-ray absorption spectroscopy (XAS) at the S K-edge and Au L3-edge. First, a thorough assignment of all sulfur contributions to the XANES spectrum was performed, distinguishing for the first time long and short staple motifs. Following that, a structural comparison of doped systems using XANES and EXAFS confirmed the unaltered Au25 structure, except for some slight influence on the Au–S bonds. Additionally, an intact staple motif was confirmed after incorporation of rigid dithiol BINAS by both XANES and EXAFS. This finding agrees with a BINAS interstaple binding mode predicted by calculation, which does not perturb the cluster structure.