Conducting polymers, such as polyaniline (PANi) and polypyrrole (PPy), and their nanocomposites, are desired in a wide range of applications, including supercapacitors, lithium ion battery, chemical sensors, biosensors, barrier thin films, and coatings, because of their interesting electrical and electrochemical properties. It is well known that the properties of polymer nanocomposites depend on their chemical structure, as well as their microstructure, yet scientists and engineers have not fully understood how to properly control the structure of polymer nanocomposites. In this study, it is shown that the structure of polyaniline–montmorillonite clay nanocomposites (PACN) can be controlled by varying the ammonium persulfate (APS, oxidant) concentration. The structure of polyaniline and Cloisite 20A clay are, therefore, profoundly affected during the synthesis of PACN nanocomposites. The thickness of polyaniline crystal decreased with increasing oxidant concentration. Fourier transform infrared spectroscopy (FTIR) was used to determine the oxidation state of PANi. The structure of the nanocomposites was studied by using scanning electron microscopy (SEM), transmission electron microscopy (TEM), wide-angle X-ray diffraction (WAXD), wide-angle X-ray scattering (WAXS), and small-angle X-ray scattering (SAXS). Electrochemical impedance spectroscopy (EIS) analysis of polyimide nanocomposite coatings containing PACN with varying levels of intercalation and exfoliation indicate that the coating impedance decreased with exposure time for some coating systems. It is shown that polyimide–PACN nanocomposite coating containing highly intercalated clay was more durable and maintained constant impedance after 20 weeks of exposure in a corrosive medium.