Bacillus cereus strain C1L, screened from the rhizosphere of Lilium formosanum, prevents severe lily leaf blight. The purpose of this study was to formulate a new biopesticide by microencapsulating the C1L strain to enhance residual stability. In addition, since the viable cell number of Bacillus cereus C1L is an important factor affecting the biological effects of this fungicide, this study also used the response surface methodology and sequential quadratic programming methods to optimize the best formula for maximum viability of Bacillus cereus C1L microencapsulated by spray drying. Optimization results revealed that the strain could maintain 42% viability with 18.3% maltodextrin and 12.5% gum arabic as coating materials and spray drying at an outlet temperature of 73.5 ºC. A comparison with chemical pesticides showed that maneb was the most efficient disease inhibitor, followed by B. cereus C1L encapsulated by spray drying. The chemical pesticide probenazole and B. cereus C1L encapsulated by extrusion revealed no significant differences in disease control.