In this study, horseradish peroxidase (HRP) enzyme was immobilized on Pd(II) containing polymeric microspheres by adsorption method and used for the decolourisation of Methyl Orange (MO) and Rhodamine B (RB) dyes. The synthesized microspheres were characterized by Fourier Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscopy-Energy Dispersive X-ray (SEM/EDX), Thermal Gravimetric Analysis (TGA). The effects of pH, dye concentration, temperature, and H2O2 concentration on the decolourisation of MO and RB were determined. According to the results of various parameters studied, when 2-AEPS-napht-HRP support was used, MO and RB were biodegraded to 69.72% and 80.65%, respectively, within 60 min. When 2-AEPS-napht-Pd-HRP support was used, MO and RB were biodegraded to 58.35% and 90.81%, respectively, under optimum conditions. When the reproducibility results of the immobilized supports were examined, it was observed that they remained efficient during the first five reusability cycles and even reached 65% decolourisation efficiency after the 9th reuse. The immobilized enzyme (2AEPS-npht-HRP and 2AEPS-npht-Pd-HRP) showed remarkable resistance to higher temperatures compared to the free enzyme.