Ganoderma boninense is a causal pathogen of basal stem rot disease, a serious problem of oil palm production. For successful infection, Ganoderma species produce extracellular lignocellulosic enzymes that are required to penetrate the host tissue. Therefore, the inhibition of fungal growth and lignocellulosic enzyme activity could reduce the disease severity. In this research, physical factors and chemical nutrients that influence lignocellulosic enzymes were screened by the Plackett–Burman design. An effective chemical fungicide was selected by the poisoned food technique. Regarding biological factors, Trichoderma virens K1-02 was evaluated for its antagonistic potential against G. boninense K4/2. The result found that the affective factors on this pathogen were temperature (physical factor), boron and potassium (chemical nutrient), and mancozeb (chemical fungicide). The increase in temperature up to 40 °C had negative relationships with cellulase and laccase of G. boninense K4/2. The increase of potassium to 14.0 mg/mL and boron to 0.2 mg/mL inhibited cellulase and xylanase activities. Mancozeb in a concentration of 1.0 mg/mL inhibited G. boninense growth, but T. virens K1-02 could grow and produce spores on this fungicide medium. T. virens K1-02 had the antagonist potential against G. boninense K4/2 with percentage inhibition by volatile antifungal compound of 12.59 ± 2.10, percentage inhibition under dual culture method was 80.86 ± 3.29, and antifungal enzyme production of 0.33 ± 0.27 and 1.00 ± 0.22 U/mL for chitinase and beta-1,3-glucanase, respectively. For the correlation between these factors, temperature and mancozeb were negatively correlated to T. virens K1-02. However, there were no correlations between temperature, potassium, boron, and mancozeb. Furthermore, the research results will help growers develop integrated disease management strategies for controlling basal stem rot disease in oil palm.