Upon contact of sensor surfaces with complex biological samples containing a variety of different proteins, non-specific adsorption hampers the high-sensitive detection of the analyte in question. To substantially decrease the impact of non-specific adsorption at thiol-based self-assembled monolayers, a chemical lift-off process is introduced. A sequence of local hydrolysis of isooctyl 3-mercaptopropionate, covalent binding of an antigen against the Epstein–Barr virus (EBV), stepwise incubation with a serum sample possibly containing the EBV antibody and an enzyme-labeled anti-human antibody is completed with a lift-off by integral hydrolysis of the remaining ester groups at the self-assembled monolayer. The cleavage of the ester removes any non-specifically bound protein during a following stringent washing step. The substantial improvement of the detection limit of an electrochemical immunoassay against EBV using native recombinant antigens, their immobilization after local deprotection using a scanning electrochemical microscope (SECM) and the local read-out using the generator–collector mode of SECM with redox cycling amplification demonstrates the successful application of the proposed lift-off procedure.