Soybeans are an essential commodity for Indonesian people, who still rely on imports to meet national needs. Agroforestry is one of the solutions to increase soybean production. Agroforestry systems have different conditions from agricultural land in general. Trees such as pine and mahogany can influence the presence of other organisms that can potentially interfere with crop growth. Bacterial pustule is an important disease of soybeans caused by Xanthomonas axonopodis. The research aimed to observe disease incidence in soybeans in pine and mahogany agroforestry systems. This research was conducted at KHDTK Forestry-Alas Bromo in Karanganyar, Central Java, Indonesia. The study used a completely randomized block design with six varieties of soybeans planted in an agroforestry system with mahogany and pine fields. The varieties were Argomulyo, Dena-1, Dena-2, Denasa-1, Denasa-2, and Devon. The research showed that no pustule bacteria were observed in the agroforestry system with pine. However, soybeans in agroforestry systems with mahogany were infected by pustule bacteria with an incidence of up to 40%. No infection on agroforestry soybeans in pines is presumably related to the microclimate condition. The microclimate conditions in pine agroforestry are more open and hot, while in mahogany, agroforestry conditions are more humid and less exposed to sunlight.