In this study, environment-friendly cost-effective, non-toxic, and reusable strategy was developed using Bacillus subtilis (a GRAS-grade bacterium, isolated from the Korean traditional food, Kimchi) immobilized in edible alginate bead composite for the reduction of ochratoxin A (OTA) toxin from red wine. Initially, B. subtilis-immobilized sodium alginate beads reduced 90% of the OTA from the culture medium (pH 3 and 25% NaCl), and the reduction in the OTA content increased as the pH decreased and the NaCl concentration increased. Additionally, the immobilized sodium alginate beads when added to red wine spiked with OTA, resulted in OTA reduction by 78.50 ± 0.49% after 1 h. Free Bacillus subtilis cells showed OTA reduction by 81.70 ± 1.91% but required higher number of cells, thus was not a cost effective approach. Furthermore, simple cleaning the beads with ethanol allowed them to be reused and renewed at least 10–20 times with a significant OTA reduction ability. These findings suggest the potential application of B. subtilis-immobilized alginate beads in OTA reduction from red wine samples, and the strategy could be applied for other types of liquid foods.