Clarification of fruit juice is a pivotal step in the juice and beverages industries which enhance appearance and marketability. In the present study, a pectinolytic enzyme producing Bacillus subtilis strain BK-3 was isolated from Bakreshwer hot spring. The pectinase production was increased in a liquid medium, which contains citrus peel waste as a substrate. Pectinase production was 2.47 fold enhanced than initial production after the response surface methodology (RSM) approach. SDS PAGE result shown that the molecular weight of pectinase was ~33 kDa. The pH and temperature optima were 5.0 and 50 °C, respectively, and pectinase presented stability at a broader pH (4-10) and temperature range (30–60 °C). The metal ions KCl and MnCl2 significantly affected enzyme activity in a positive direction, whereas the solvent inhibited the biocatalytic performance. The Km and Vmax of pectinase were 0.4770 mg mL-1 and 43.46 IU mL-1, respectively. After the pectinase treatment in various fruit juice (black mulberry, apple, orange, and pineapple), clarity and reducing sugar were increased, and turbidity was decreased. All this characteristic of pectinase exhibit a good prospect for bio-industrial exploration.