In this study Bacillus subtilis PTCC 1023 was used for the production of protopectinase using soybean based media. The use of isolated soybean protein (ISP) and soybean flour resulted in similar protopectinase production and growth rates. The effect of medium composition on protopectinase production was studied using central composite design (CCD) methodology. The change in the concentration of ISP (1-7%), glucose (0-10%), and phosphate (0.1-0.3 M) was found to affect the protopectinase activity (response variable) after 24 hr of cultivation. In the range studied, ISP and glucose had a negative effect on the response variable, whereas phosphate had a positive effect. A statistically significant interaction was identified between phosphate and ISP, suggesting that correct optimization of medium formulation in this case can only be obtained using factorial design of experiments. Protopectinase activity exceeding 215 U/mL was obtained in a medium containing 4% ISP, 0.3M phosphate, and no added sugar.