In this study, cheese whey – a nutrient-rich industrial waste was utilized as a low-cost fermentation medium for the growth of Bacillus subtilis and nattokinase production. The nattokinase yield (caseinolytic activity) using cheese whey (789.93 U ml−1) was 5 %–7 % less compared to glucose- or lactose-based synthetic media (833.44 and 850.84 U ml−1, respectively). Effect of nitrogen supplementation (yeast extract, tryptone, and peptone) on nattokinase yield was tested adopting an L9 (33) Taguchi experimental design, which revealed yeast extract as the best nitrogen source. Yeast extract supplementation (10 g l-1) to cheese whey increased the caseinolytic activity to 833.43 U ml−1, making it comparable to lactose- and glucose-based synthetic media, while lowering the medium cost by 55–60 %. A dynamic model incorporating logistic growth, substrate utilization and Luedeking-Piret product formation kinetics across all carbon-sources offered good agreement (R2 > 0.93). The estimated maximum specific growth rate on lactose-based synthetic medium (0.204 h−1), or yeast extract supplemented cheese whey medium (0.201 h−1) were better than that of the glucose-based synthetic medium (0.122 h−1). A similar observation on the growth associated product formation parameters offers insight on medium selection process. Overall, this study suggested that cheese whey could be utilized as a low-cost medium for nattokinase production.