The initiation of corrosion can be triggered by defects in the adsorbed layer of organic inhibitors. A detailed knowledge of the intermolecular forces between the inhibitor molecules and the interfacial bonding will be decisive to unravel the mechanisms driving the corrosion initiation. In this work, adsorbed organic layers of 2-mercapto-5-methoxybenzimidazole (SH-BimH-5OMe) and 5-amino-2-mercaptobenzimidazole (SH-BimH-5NH2) were compared regarding their performance mitigating copper corrosion. Atomic force microscopy was used to address the stability and intermolecular forces of the self-assembled monolayers, using imaging and force measurement modes. For a film formed by amino-derivative molecules, a gold-coated tip frequently picked up individual molecules (molecular fishing) in force-distance measurements. For layers of the methoxy-derivative, no fishing events were observed, pointing to a constant functional layer. X-ray photoelectron spectroscopy revealed that SH-BimH-5OMe molecules form a stronger bond with the surface and more stable SAM layers on Cu surfaces as compared to SH-BimH-5NH2 molecules. Results of computational density functional theory modeling and electrochemical corrosion tests are in line with the microscopy and spectroscopy results. In particular, with aid of computational modeling the less ordered structure of the SH-BimH-5NH2 monolayer is attributed to dual bonding ability of SH-BimH-5NH2 that can adsorb with either S or NH2 groups.