In present study polypyrrole-zirconium(IV)selenoiodate cation exchanger nanocomposite (PZrSeI-CENC) was employed to immobilize ginger peroxidase (GP) via strong electrostatic interactions. Fourier transform infrared spectroscopy, transmission electron microscopy and scanning electron microscopy was done to characterize the PZrSeI-CENC before and after immobilization of GP. PZrSeI-CENC bound GP exhibited very high activity yield of around 96%. Immobilized GP was less sensitive to the changes in pH and temperature compared to free GP. In stirred batch processes immobilized GP was able to decolorize around 96% of the Methyl Violet 6B (MV 6B) dye after 3 h of incubation whereas only 81% of the dye was decolorized by free GP under identical experimental conditions. Immobilized GP exhibited excellent reusability in the stirred batch process and decolorized around 60% of the dye even after its 10th repeated use. Furthermore, V-max. of PZrSeI-CENC bound GP was amplified 10 times which is mainly attributed to polypyrrole aided enhanced electron shuttle system of the enzyme. A degradation pathway was proposed in compliance with gas chromatography-mass spectroscopy analysis that confirms the degradation of MV 6B into low molecular weight products. The genotoxic assessment revealed a significant reduction in toxicity of dye after treatment with nanocomposite bound peroxidase.