The molecular structure and organization of self-assembled monolayers (SAMs) and multilayer films grafted onto Au/Si(1 1 1) surfaces of mononuclear transition metal dialkynyl bridged Pd(II) complexes trans-[HS-Pd(PBu3)2-SH] (1), trans-[HS-Pd(PBu3)2(–CC–C6H5)] (2) and of the binuclear complex trans, trans-[HS-Pd(PBu3)2(–CC–C6H4–C6H4–CC–Pd(PBu3)2-SH] (3), have been investigated by extended X-ray absorption fine structure spectroscopy in total reflection conditions (reflEXAFS). ReflEXAFS analysis of the data lead to determine the local structure around Pd atoms, assessing the square-planar geometry around the transition metal in the multilayers case, preserved in the monolayer regime. The investigation on the SAMs also provided the assessment of the S–Au bond length and Pd–S–Au bond angle and on the molecular orientation on the gold substrate of the complexes, confirmed by quantum chemical calculations.Graphical abstractThe molecular structure and organization of organometallic Pd(II) thiolates SAMs and multilayers on Au/Si(1 1 1) were investigated by reflEXAFS. For SAMs, S–Au bond lengths, Pd–S–Au bond angles and molecular orientations were assessed.Research highlights► Organometallic Pt(II) thiolates deposited as SAMs and multilayers on gold. ► Molecular structure and organization of SAMs and multilayers studied by reflEXAFS. ► SAMs S–Au bond lengths, Pd–S–Au bond angles and molecular orientations are assessed.