Pests are one of the limiting factors in increasing soybean production. Pest control carried out by farmers using pesticides is feared to threaten the sustainability of soybean production in Indonesia. This study aimed to identify the effect of different pest management systems and various soybean varieties on pest population dynamics, abundance and diversity of natural enemies, plant damage, and soybean production. A split plot design with three replications was applied, where the main plot was pest management systems i.e. (1) control (which received neither chemicals nor integrated pest management), (2) chemical control, and (3) integrated pest management, and the sub-plot was soybean varieties i.e. (1) Anjasmoro, (2) Demas 1, and (3) Dering 1. Results indicated that variety affects pest diversity and abundance, however, it affected leaf damage, pod damage, and production. The pest management systems influenced the diversity and abundance of pests and natural enemies, plant damage, and production. Interaction between variety and pest management system affected plant damage. We conclude that the use of resistant varieties combined with integrated pest management could reduce plant damage, maintain the natural enemy population, and optimize soybean production.