Oil palm is one of the most important crops in Malaysia and plays a significant role in the agricultural and economic development of the country. Basal stem rot (BSR) caused by Ganoderma boninense is the biggest threat to oil palm production and has been documented to cause huge losses to the oil palm industry in Malaysia. There is yet to be an effective control measure for BSR disease. Endophytic fungi have been previously studied and identified as potential biological control agents (BCA) for many crop diseases. The overall success of biocontrol depends on the effectiveness of the method used for searching and screening biocontrol agents. Endophytic fungi, Hendersonia toruloidea GanoEF1, Amphinema GanoEF2 and Phlebia GanoEF3, were isolated from more than 500 culturable endophytic fungal samples isolated from the roots of healthy oil palms in Malaysia. These isolates were further formulated into powder and granular forms, which profoundly affected the efficacy of BSR disease control. Isolate H. toruloidea GanoEF1 was found to be a novel and promising biological control agent against G. boninense; therefore, this isolate was further developed for commercialisation. The process of mass production of the endophytic fungus, H. toruloidea, as GanoEF biofertiliser has been commercialised. The commercialisation package involves mass production of H. toruloidea GanoEF1 inoculum, preparation of a carrier, mixing the inoculum into the carrier, and packaging the final product. In greenhouse and field trials, oil palm seedlings treated with GanoEF biofertiliser showed a positive outcome in controlling infection and growth of G. boninense. The use of endophytes in the form of a formulated product is preferred and sought after as such preparations offer many advantages during application in the field.