Safe, low-cost structurally colored materials are alternative colorants to toxic inorganic pigments and organic dyes. Colloidal amorphous arrays are promising structurally colored materials because of their angle-independent colors. In this study, we focused on precise tuning of the chromaticity by preparing bilayer colloidal amorphous arrays through electrophoretic deposition (EPD). Systematic investigations with various EPD conditions clarified the contributions of each condition to the EPD process and the competing electrochemical reactions, which enabled us to prepare well-colored coatings. EPD films composed of colloidal amorphous array bilayers were successfully synthesized with controlled film thickness. Chromaticity of the films was found to be precisely controlled by the EPD duration. We believe that this understanding of the EPD process and its application to synthesis of structurally colored bilayer films will bring structurally colored materials closer to practical industrial use.