The outbreak of rice plant diseases can be effectively suppressed in organic farming systems. However, the mechanisms of disease suppression by organic farming systems are not well understood. When Burkholderia-infected rice seeds were sown and cultivated on nine organic-farmed soils which were supplied by nine independent organic rice farmers or standardized commercial conventional soils, the emergence of bacterial seedling diseases was suppressed to equivalent degrees in nine organic-farmed soils, whereas the diseases occurred in two commercial conventional soils. In any organic or commercial conventional soil sown with healthy rice seeds as a control, the diseases did not appear. Upon physicochemical analysis of the nine organic-farmed soils, component common to these organic-farmed soils seemed to not be directly associated with disease-suppressive activity. However, microbiome analyses indicated that the bacterial population in these nine organic-farmed soils was more diverse than those in commercial conventional soils. Intriguingly, the diverse bacterial population structures of organic-farmed soils were preserved after irrigating and sowing rice seeds, but that of commercial conventional soils was clearly changed by them. Thus, organic-farmed soils seem to maintain robust bacterial populations despite the irrigation and seedling growth. Indeed, pathogenic Burkholderia in infected rice seeds also did not proliferate in the seedling grown on organic-farmed soils. Taken together, the common feature of organic-farmed soils might be the correlation between bacterial seedling disease-suppressive activity and higher robustness of the diversified microbiome.