Nanoparticle‐imprinted matrices (NAIMs) were prepared using ammonium‐terminated SiO2 nanoparticles (NPs) as templates initially attached to activated glassy carbon. After electrodeposition of a matrix of polyplumbagin and polyphenol, the selectivity of the polymer matrix was tuned towards the ligand shell of the Au analyte NPs by conjugate addition of substituted thiols to the plumbagin moiety within the matrix. The reactions were followed by cyclic voltammetry (CV) and the presence of thiols and amino groups in the film was verified by X‐ray photoelectron spectroscopy (XPS). After dissolution of the template NPs, the matrix had complementary cavities for the uptake of Au NPs. The amount of Au NP inside the cavities was quantified by the charge transferred during electrodissolution of the Au NPs in 3 M KCl in linear sweep voltammetry, which depended on the covalent modification of the polyplumbagin matrix, the pH during uptake and the size of the Au analyte NPs. The NAIM system modified with 1,2‐ethanedithiol showed the best uptake with 9.6×107 NPs cm−2 at pH 10, which is five times higher than the uptake of the same matrix at pH 5. In contrast, the cysteamine‐modified NAIM exhibited the highest uptake at pH 5.