Ganoderma has always been the main cause of basal stem rot (BSR) in many countries including Indonesia. Many approaches have been made, such as physical, chemical, and biology approaches using endophytic microorganisms. This study uses Ganoderma vaccine/ Biofungicide CHIPS to control Ganoderma and MOAF fertilizer as a nutrition source in oil palms that are severely infected by Ganoderma. Experiment is conducted in an oil palm plantation at Kecamatan Bilah Hilir, Kabupaten Labuhan Batu, Sumatera Utara, Indonesia. This plantation is a sandy mineral soil, which is a former swamp area. Because of the low contour of the land, the areas are often inundated by floods for more than 1 month from the end of the year to the beginning of the year. This study aims to eradicate basal stem rot (BSR) disease in the areas. Because of the flooded area, the soil is quite damp and equal dispersion of Ganoderma spores occurs massively throughout the whole area. We conducted the study for 4 years (2017 to 2020), using Ganoderma vaccine/Biofungicide CHIPS in 3 blocks: D4, D5, and C3 as study area and block C6 as control block (without CHIPS). Results of this study showed the productivity reached 79,12 to 94,02% of the PPKS (Indonesia Oil Palm Research Centre) standard production. Although in unfavorable environmental conditions, these numbers show a very satisfying result as it compensates for healthy normal oil palm production, while experiment blocks using inorganic fungicides and Trichoderma, the productivity decreased from year to year. The combined application of Organic fertilizer MOAF for nutrient sources with Ganoderma vaccine /Biofungicide CHIPS is very effective against the spread of basal stem rot (BSR) diseases in oil palms even in unfavorable environments as in flooded areas.