In industrial processes, effective degradation of polygalacturonic acid using immobilized pectinase is preferred over free one due to its stability and efficient functional reuses. Pectinase was covalently conjugated to the surface of cyanuric chloride functionalized chitosan encapsulated magnetite nanoparticles. The results obtained of various analytical tools and biochemical studies demonstrated successful synthesis and immobilization processes, high immobilization efficiency and loading capacity. The circular dichroism (CD) results of free and immobilized pectinase revealed the partial decreases in the α-helices and β-sheets, and marginal increases in the unordered elements contents of pectinase upon the immobilization onto FeO@Ch-CC nanoparticles, along with stability improvement. The immobilized pectinase was retained about 60% of its initial catalytic activity after 13 recycles at optimum conditions (40 °C, pH 4.5). The storage stability of pectinase was increased due to immobilization, after 75 days storage at 4 °C, the free and immobilized enzyme retained 43% and 74% of the initial activity, respectively. The immobilized pectinase showed higher storage stability and better performance at wider ranges of pH and temperature, compared to free pectinase.