A benzylic amide macrocycle containing a pyridine moiety (macrocycle 2) and a related benzylic amide macrocycle-based molecular shuttle (naphthalimide rotaxane) with two pyridine moieties on the macrocyclic unit were grafted onto a self-assembled monolayer (SAM) of 11-mercaptoundecanoic acid (11-MUA) on gold. X-ray photoelectron spectroscopy (XPS) indicates that the molecules are linked to the SAM by hydrogen-bonding. Electrochemical investigations show that the self-assembled monolayer is densely packed and well ordered and allows the estimation of the average thickness of the SAM alone and of the SAM functionalized with either macrocycle 2 or with naphthalimide rotaxane. The estimated thickness values suggest that the 11-MUA chains in the SAM are tilted with respect to the surface normal, as expected for ordered and stable SAMs, whereas the rotaxane molecules are oriented with the thread parallel to the SAM surface and macrocycle plan preferentially perpendicular to the surface. The photophysical studies of the naphthalimide rotaxane grafted onto the SAM on gold demonstrated that fluorescence is partially quenched but still remains easily measurable because the presence of the SAM reduces the quenching effect of the metal substrate. Moreover, the photophysical analysis clearly indicates that the naphthalimide part of the rotaxane strongly interacts with the carboxylic groups of the SAM, in agreement with the orientation of the molecule obtained from the electrochemistry.