A host-guest equilibrium involving ferrocenyl alkanethiols-thio β-cyclodextrin mixed self-assembled monolayers (FcCnS-/Cn′S-/β-CD-Au SAMs) is investigated using molecular dynamics (MD) simulations. In this work, we focus on the effects of the alkyl spacer length of the ferrocene adsorbates on the complexation behavior. Our simulations show that the formation of host-guest complexes is observed from C12 chain length Fc-thiols whereas no effect is obtained with shorter alkyl chains (FcC11S-Au). Furthermore, we underscore that the presence of the alkyl thiol chains in the ferrocene derivatives largely prevents the deeper insertion of the ferrocene moieties into the β-CD cavity. More details are reported about the impact of the oxidation process on these monolayers. In fact, it appears that Fc+ is less inserted into the β-CD cavity than Fc in aqueous solution. Nevertheless, a partial inclusion of the Fc+ residue in the cavity of the β-CD is highlighted. In fact, the position of the Fc+ into the host cavity allows a spatial location that favors both interactions with water and β-CD. The potential of mean force (PMF) characterizing the association process in aqueous solution confirms a weak association between Fc+ and C5S-/β-CD-Au SAMs. The effects of both the coadsorbed chains and the positive charge of the electrode surface on the stability of this inclusion complex are also reported.