This study has focused on the development and application of silicate coated magnetic nanoparticles functionalized by Pomegranate peel extract (PPE). Fe3O4 nanoparticles fabricated through the co-precipitation method and coating with silica then mixing with pomegranate peel extract. Afterward, Fe3O4@SiO2-PPE NPs were characterized by FT-IR, SEM, XRD and TEM. The obtained Fe3O4@SiO2-PPE nanostructure combined with H2O2 were employed as Fenton- like nanocatalyst in dye treatment processes. The effects of several factors including nanocatalyst amount, time period, temperature and H2O2 amount were measured simultaneously using chemometrics techniques. The Box-Behnken design (BBD) and response surface methodology (RSM) were used to explore the optimum conditions providing the highest decolorization efficiency. Under the optimum conditions, the decolorization efficiency toward methyl blue and methyl orange dyes were obtained > 99%. The obtained results indicated that the superparamagnetic nanocatalyst could be applied as a green and highly effective material for the degradation and decolorization of different carcinogenic azo dyes in real water samples. Reusability experiments has been performed for 8 consecutive runs.