Objective Pectinase is an industrially important enzyme which is employed in an array of commercial processes; cost of production, however, impedes its application. The main objective of this study was to design a two-layered strategy for the reduction of production cost, firstly by using a yeast co-culture in an immobilized form on an agricultural waste matrix, corncob (CB), secondly by utilizing orange peels (OP) as substrate. Results Two yeast strains, Saccaromyces cerevisiae MK-157 and Geotrichum candidum AA15 were cultivated as mono-, as well as, co-culture after immobilization on CB and pectinase production was monitored. Initial experiments revealed that co-culture is beneficial to get sustainable product in subsequent 2nd and 3rd production cycles. The factors affecting pectinase production in consecutive three production cycles were studied by employing Plackett-Burman design and the significant factors were optimized through Box-Behnken design. Under optimized conditions, 17.89 IU mL(-1) of pectinase was obtained. Scanning electron micrographs presented damaged immobilized yeast cells on CB after the 3rd production cycle. Conclusion The pectinase production was improved substantially by using immobilized co-culture and hence the strategy was found effective at lab scale. Since, pectinase is applied in orange juice clarification, therefore, the study can be extended to move forward towards circular economy.