Molecular assemblies (MAs) of oligofurans and oligothiophenes were formed from solutions on various substrates. These films were obtained by alternating deposition of organic chromophores (oligofurans or oligothiophenes) and a palladium salt. These coordination-based MAs were characterized by UV/Vis spectroscopy, spectroscopic ellipsometry, atomic force microscopy (AFM), X-ray reflectivity (XRR), X-ray photoelectron spectroscopy (XPS), and electrochemistry. The MAs exhibit similar electrochemical behavior and their growth and structure are apparently not affected when different organic template layers are used. The density of the MAs is a function of the structure of the molecular component. The oligothiophene density is approximately 50 % higher than that observed for the oligofuran-based assemblies. The optical and electrochemical properties of the MAs scale linearly with their thickness. The UV/Vis data indicate that upon increasing the film thickness, there is no significant conjugation between the metal-separated organic chromophores. DFT calculations confirmed that the HOMO–LUMO gap of the surface-bound oligofuran and oligothiophene metal oligomers do not change significantly upon increasing their chain length. However, electrochemical measurements indicate that the susceptibility of the MAs towards oxidation is dependent on the number of chromophore units.