Agarwood is a scarce and highly prized resinous material, revered for its medicinal properties and distinctive aroma profile. Traditional medical manuscripts meticulously document their application in pain relief and the alleviation of gastrointestinal distress. Agarwood is formed in Aquilaria trees (Thymelaeaceae) as a response to external stimuli, a natural process that is typically slow and inefficient. Recent scientific research has revealed the significant role of endophytic fungi in enhancing the formation of agarwood. Metabolic analysis studies have identified 486 metabolites associated with these fungi. Among them, 54 compounds were produced directly by the fungi themselves, while 432 were generated through the metabolic reprogramming of the host tree induced by the fungi. These metabolites exhibit a diverse range of biological activities, such as potent anticancer and antioxidant effects. However, the mechanisms underlying the interactions between these fungi and their host warrant further investigation. This review collates more than six decades of research into the phytochemical characteristics and therapeutic potential of these metabolites, laying a solid groundwork for the development of new drugs and biotechnological applications in the future.