Agarwood formation in Aquilaria malaccensis could be artificially stimulated by fungal infection. Furthermore, A. malaccensis adapts to this infection by developing typical included phloem boundary within xylem tissues. Naturally synthesized agarwood requires a lengthy process of up to 30 years, which impedes its continuous production. Therefore, recent effort has been allocated to the elucidation of agarwood formation to stimulate its process rapidly. In this study, we artificially induced agarwood formation by injection and inoculation of cultivated Aquilaria malaccensis with four strains of Fusarium solani isolated from different places in Indonesia. The results showed that A. malaccensis responded differently upon wounding and fungal inoculations compared to healthy trees. All wounded and inoculated samples resulted in the formation of typical discoloration zone surrounding injection sites. Further anatomical observation revealed that both samples also developed included phloem structures in which resinous agarwood compounds were accumulated. Gas chromatography-mass spectrometry (GC-MS) analysis of the inoculated samples yielded some important agarwood compounds such as tridecanoic acid, alpha-santalol, and spathulenol, which were not present in both healthy controls and only wounded samples. Notably, one of the tested F. solani, strain Gorontalo displayed promising results as a candidate for artificially induced agarwood formation in A. malaccensis in terms of color, odor, and chemical constituents.