The research aimed to determine the effects of the doses of organic fertilizer and the addition of Bacillus spp. on the changes in soil chemical properties, NPK nutrient uptake, vegetative and generative growth, and resistance to stunting as well as yields of superior and local cultivars of organic rice. Soil samples were taken before and after one week of treatments. Meanwhile, observation of plant samples was carried out from seven days after planting until harvest, then these samples were taken at the end of the vegetative and generative growth stage. This research was conducted in Kebonagung, Imogiri, Bantul from October 2020 to May 2021. The treatments consisted of the application of organic fertilizer at doses of 0 tons/ha, 5 tons/ha, and 10 tons/ha and the addition of Bacillus spp. on the superior and local cultivars of organic rice. The results suggested that the treatment of 10 tons/ha fertilizer combined with Bacillus spp. affect the organic C, CEC, and availability of soil NPK. The treatment also increased the NPK nutrient uptake and improved plant resistance to stunting diseases due to RRSV. Among all the treatments applied, the highest yield of ‘Padjajaran’ (12.13 tons/ha) and ‘Mentik Wangi’ (11.62 tons/ha) cultivar was obtained when treated with 10 tons/ha fertilizer combined with Bacillus spp. and 10 tons/ha fertilizer without Bacillus spp., respectively.