The occurrence of 17α-ethinylestradiol (EE2) in the environment and its removal have drawn special attention from the scientific community in recent years, due to its hazardous effects on human and wildlife around the world. Therefore, the aim of this study was to produce an efficient enzymatic system for the removal of EE2 from aqueous solutions. For the first time, commercial silica nanopowder and 3D fibrous chitinous scaffolds from Aplysina fistularis marine sponge were used as supports for horseradish peroxidase (HRP) immobilization. The effect of several process parameters onto the removal mechanism of EE2 by enzymatic conversion and adsorption of EE2 were investigated here, including system type, pH, temperature and concentrations of H2O2 and EE2. It was possible to fully remove EE2 from aqueous solutions using system SiO2(HRP)–chitin(HRP) over a wide investigated pH range (5–9) and temperature ranges (4–45 °C). Moreover, the most suitable process conditions have been determined at pH 7, temperature 25 °C and H2O2 and EE2 concentrations equaling 2 mM and 1 mg/L, respectively. As determined, it was possible to reuse the nanoSiO2(HRP)–chitin(HRP) system to obtain even 55% EE2 degradation efficiency after five consecutive catalytic cycles.