This study uses an overall evaluation criterion for improving the immobilized bead reusability and extracellular enzyme production by immobilized cells by assigning relative weightage to bead reusability, enzyme production, and cell leakage. Initially, alkaline protease production by alginate-immobilized Bacillus circulans (MTCC 6811) was analyzed using L18 orthogonal array (OA). The resultant optimized parameters were further fine-tuned with L9 OA experimentation. At L18-OA analysis, inoculum level and CaCl2 had least influence at individual level. At the interactive level, incubation time revealed maximum and minimum interaction with sodium alginate and glucose concentration, respectively. L9 experimentation indicated that glucose concentration contributed the major influence on protease production followed by matrix material and incubation time at the individual level, and at the interactive level, matrix concentration played a vital role by interacting with incubation time, inoculum, and CaCl2 concentration. All selected input parameters showed significance either at individual level or interactive in both OAs. Scanning electron microscopy analysis showed bacterial morphology variation with variation of matrix concentration. Overall, glucose concentration depicted a major influence at the individual level for the enzyme production. Significant improvement, approximately 147%, in enzyme yield was observed. Economic enzyme production by immobilized B. circulans is regulated by interactive influence of fermentation parameters, which influence the immobilized bead stability, reusability, and enzyme yield.