The difference in the heterogeneous binding of Mg²⁺, Ca²⁺ and Sr²⁺ ions by 1-thioglycerol (TG) and 1,4-dithiothreitol (DTT) spontaneously adsorbed monolayers on Au has been studied following the changes in the double layer capacity. A mathematical treatment, based on calculating the electrochemical potential difference at the monolayer–electrolyte interface, has followed our recent work which dealt with the acid–base equilibrium at the interface as a means of calculating the pK of ionizable SAMs and their binding with Cd²⁺. Experimentally, spontaneously adsorbed monolayers of TG and DTT were assembled on Au surfaces and studied by impedance spectroscopy and alternating current voltammetry (ACV). The capacity was measured for each of the modified surfaces at increasing concentrations of the divalent metal ions separately. The goal of this study has been to examine the effect of metal ion binding by similar ligands that are differently attached onto the surface. TG and DTT monolayers differ in their flexibility, which is a result of their attachment to the surface through one and two arms, respectively. The general trend of the apparent heterogeneous association constants of the divalent metal ions, which were calculated from the capacity measurements, was substantially different from the classical Irving–Williams series that is applicable to homogeneous systems. This difference could be nicely explained by the reduction of the degree of freedom and flexibility of the attached ligands.