The development of highly selective probes for nanoparticles is required due to their nanotoxicity. The latter strongly depends on the size, structure, and interfacial properties of the nanoparticles. Here, we demonstrate that a simple approach for the selective detection of Au nanoparticles that differ in their capping agent shows very high promise. Specifically, gold nanoparticles stabilized by each of the three different isomers of mercaptobenzoic acid (MBA) were imprinted in a soft matrix by adsorption of the nanoparticles, followed by filling the non-occupied areas through electropolyermization of an aryl diazonium salt (ADS). Nanocavities bearing the shape of the Au nanoparticles were formed upon the electrochemical dissolution of the nanoparticles, which were used for the reuptake of the Au nanoparticles stabilized by the different isomers. High reuptake selectivity was found where the originally imprinted nanoparticles were recognized better than the Au nanoparticles stabilized by other MBA isomers. Furthermore, an imprinted matrix by nanoparticles stabilized by 4-MBA could also recognize nanoparticles stabilized by 2-MBA, and vice versa. A detailed study using Raman spectroscopy and electrochemistry disclosed the organization of the capping isomers on the nanoparticles as well as the specific nanoparticle-matrix interactions that were responsible for the high reuptake selectivity observed. Specifically, the Raman band at ca. 910 cm −1 for all AuNP−matrix systems implies the formation of a carboxylic acid dimer and thus the interaction of the ligands with the matrix. These results have implications for the selective and simple sensing of engineered nanoparticles.