In the present work, enzymes pectinase and naringinase were simultaneously co-immobilized on an eco-friendly chitosan coated magnetic nanoparticles (chitosanMNPs) by cross-linking using chitosan as a macro-molecular cross-linker. The maximum activity recovery of both enzymes in the co-immobilized form was obtained at chitosanMNPs to enzymes ratio of 1:3, 3% cross-linker concentration and 150 min cross-linking time. The synthesized MNPs before and after co-immobilization were characterized using different techniques. The prepared biocatalyst was found spherical with an average size below 200 nm and showed supermagnetic property with saturation magnetization of 38.28 emu/g. The optimum pH and temperature of both enzymes in co-immobilized form was found at 5.5 and 65 °C. The prepared biocatalyst exhibited an improved thermal stability with 1.8-fold increase in the half-life. The secondary structural analysis revealed that, prepared co-immobilized biocatalyst undergone changes in the conformational and structural rigidity due to macro-molecular cross-linker. The co-immobilized biocatalysts were evaluated for one pot clarification and debittering of grapefruit juice and found ~52% reduction in turbidity and ~85% reduction in the naringin content. The co-immobilized enzymes were recycled up to 7 cycle and can be easily stored at room temperature for 30 days retaining up to 64% and 86% residual activities respectively.