The synthesis of robust intrinsically conducting polymers (ICPs) based on nanoparticles is becoming increasingly attractive to the research community due to the unique properties of these nanocomposites. Indeed, as organic semiconductors, ICPs combine both polymer and metal properties in a single structure. This study presents an innovative approach in which the Doehlert Matrix (DM) is applied to a novel ICP nanocomposite based on polyaniline (Pani) coupled with selenium (Se) loaded mesoporous titania (TiO2) for wastewater treatment by photocatalysis. It includes both the elaboration routes of ICP nanocomposites, characterization of materials by X-ray diffraction (XRD), BET analysis, thermogravimetric analysis (TGA), RAMAN spectroscopy and Fourier transform infrared spectroscopy (FTIR) and photodegradation of methylene blue (MB) as a representative of dye pollutant. In addition, the photocatalytic process has been optimized by a novel DM conception. The effect of the pH of the solution, the catalyst dosage and the initial pollutant concentration was investigated. The optimum conditions were found to be: initial MB concentration of 15 mg/L, the catalyst dosage of 69 mg and pH of 9.6 with an operating time of 75 min, with a coefficient of determination R2 equal to 0.9985. The removal efficiency of BM was close to 97 %. The study shows that the new ICP nanocomposites improve the photocatalytic efficiency compared to pure titania and/or pure Pani. In addition, as the ternary Pani-Se-TiO2 nanocomposite could be obtained from a low-cost synthesis, it is a very promising material for use in wastewater treatment.